title: Availability: A Metric for Nucleic Acid Strand Displacement Systems.
abstract: DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Olson
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Shohei
authors.initials: S
authors.lastname: Kotani
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Padilla
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Natalya
authors.initials: N
authors.lastname: Hallstrom
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Sara
authors.initials: S
authors.lastname: Goltry
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Jeunghoon
authors.initials: J
authors.lastname: Lee
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Bernard
authors.initials: B
authors.lastname: Yurke
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: William L
authors.initials: WL
authors.lastname: Hughes
authors.affiliation: Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States.
authors.forename: Elton
authors.initials: E
authors.lastname: Graugnard
mesh_terms: D020137:Base Pair Mismatch; D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D058615:Synthetic Biology
chemical_list: D004247:DNA
keywords: DNA; availability; fraying; leakage; mutual availability; nucleic acids; reaction networks; strand displacement