title: Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids.
abstract: Locked nucleic acids (LNAs) are conformationally restricted RNA nucleotides. Their increased thermal stability and selectivity toward their complements make them well-suited for diagnostic and therapeutic applications. Although the structural and thermodynamic properties of LNA-LNA, LNA-RNA, and LNA-DNA hybridizations are known, the kinetic effects of incorporating LNA nucleotides into DNA strand displacement systems are not. Here, we thoroughly studied the strand displacement kinetics as a function of the number and position of LNA nucleotides in DNA oligonucleotides. When compared to that of an all-DNA control, with an identical sequence, the leakage rate constant was reduced more than 50-fold, to an undetectable level, and the invasion rate was preserved for a hybrid DNA/LNA system. The total performance enhancement ratio also increased more than 70-fold when calculating the ratio of the invading rate to the leakage rate constants for a hybrid system. The rational substitution of LNA nucleotides for DNA nucleotides preserves sequence space while improving the signal-to-noise ratio of strand displacement systems. Hybrid DNA/LNA systems offer great potential for high-performance chemical reaction networks that include catalyzed hairpin assemblies, hairpin chain reactions, motors, walkers, and seesaw gates.
authors.affiliation: Micron School of Materials Science & Engineering 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 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 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 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
authors.affiliation: Micron School of Materials Science & Engineering 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
mesh_terms: D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; C477371:locked nucleic acid; D004247:DNA