DNA hairpins: Fuel for autonomous DNA devices

Biophysical Journal

Volumn 91, Issue 8, 2006, Pages 2966-2975

  Green, Simon J ^a   Lubrich, Daniel ^a   Turberfield, Andrew J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; CHEMICAL REACTION KINETICS; DEVICE; DNA HYBRIDIZATION; ENERGY TRANSFER; FLUORESCENCE; HYBRIDIZATION; MEASUREMENT; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

EID: 33749510645     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.084681     Document Type: Article

References (32)

1. Yurke, B., A. J. Turberfield, A. P. Mills, F. C. Simmel, and J. L. Neumann. 2000. A DNA-fuelled molecular machine made of DNA. Nature. 406:605-608.
2. Yan, H., X. Zhang, Z. Shen, and N. C. Seeman. 2002. A robust DNA mechanical device controlled by hybridization topology. Nature. 415:62-65.
3. Li, J. J., and W. Tan. 2002. A single DNA molecule nanomotor. Nano Lett. 2:315-318.
4. Sherman, W. B., and N. C. Seeman. 2004. A precisely controlled DNA biped walking device. Nano Lett. 4:1203-1207.
5. Shin, J.-S., and N. A. Pierce. 2004. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126:10834-10835.
6. Yin, P., H. Yan, X. G. Daniell, A. J. Turberfield, and J. H. Reif. 2004. A unidirectional DNA walker that moves autonomously along a track. Angew. Chem. Int. Ed. Engl. 43:4906-4911.
7. Chen, Y., M. Wang, and C. Mao. 2004. An autonomous DNA nanomotor powered by a DNA enzyme. Angew. Chem. Int. Ed. Engl. 43:3554-3557.
8. Bath, J., S. J. Green, and A. J. Turberfield. 2005. A free-running DNA motor powered by a nicking enzyme. Angew. Chem. Int. Ed. Engl. 44:4358-4361.
9. Tian, Y., Y. He, Y. Chen, P. Yin, and C. Mao. 2005. A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew. Chem. Int. Ed. Engl. 44:4355-4358.
10. Turberfield, A. J., J. C. Mitchell, B. Yurke, A. P. Mills, Jr., M. I. Blakey, and F. C. Simmel. 2003. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90:118102.
11. SantaLucia, J. 1998. A unified view of polymer, dumbell, and oligonucleotide nearest neighbour thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
12. Bois, J. S., S. Venkataraman, H. M. Choi, A. J. Spakowitz, Z.-G. Wang, and N. A. Pierce. 2005. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 33:4090-4095.
13. Yurke, B., and A. P. Mills, Jr. 2003 Using DNA to power nanostructures. J. Genetic Programming and Evolvable Machines. 4:111-122.
14. Dirks, R. M., and N. A. Pierce. 2004. Triggered amplification by hybridization chain reaction. Proc. Natl. Acad. Sci. USA. 101:15275-15278.
15. Kuznetsov, S. V., Y. Shen, A. S. Benight, and A. Ansari. 2001. A semi-flexible polymer model applied to loop formation in DNA hairpins. Biophys. J. 81:2864-2875.
16. Shen, Y., S. V. Kuznetsov, and A. Ansari. 2001. Loop dependence of the dynamics of DNA hairpins. J. Phys. Chem. B. 105:12202-12211.
17. Goddard, N. L., G. Bonnet, O. Krichevsky, and A. Libchaber. 2000. Sequence dependent rigidity of single stranded DNA. Phys. Rev. Lett. 85:2400-2403.
18. Wallace, M. I., L. Ying, S. Balasubramanian, and D. Klenerman. 2001. Non-Arrhenius kinetics for the loop closure of a DNA hairpin. Proc. Natl. Acad. Sci. USA. 98:5584-5589.
19. Aalberts, D. P., Parman, J. M. and N. L. Goddard. 2003. Single-strand stacking free energy from DNA beacon kinetics. Biophys. J. 84:3212-3217.
20. Volker, J., N. Makube, G. E. Plum, H. H. Klump, and K. J. Breslauer. 2002. Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: implications for triplet expansion diseases. Proc. Natl. Acad. Sci. USA. 99:14700-14705.
21. Lehnert, V., L. Jaeger, F. Michel, and E. Westhof. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3:993-1009.
22. Tomizawa, J. 1984. Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell. 38:861-870.
23. Persson, C., E. Gerhart, H. Wagner, and K. Nordstrom. 1988. Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J. 7:3279-3288.
24. Paillart, J. C., R. Marquet, E. Skripkin, C. Ehresmann, and B. Ehresmann. 1996. Dimerization of retroviral genomic RNAs: structural and functional implications. Biochimie. 78:639-653.
25. Paillart, J. C., E. Skripkin, B. Ehresmann, C. Ehresmann, and R. Marquet. 1996. A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc. Natl. Acad. Sci. USA. 93:5572-5577.
26. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.
27. Stryer, L., and R. P. Haugland. 1967. Energy transfer: a spectroscopic ruler. Proc. Natl. Acad. Sci. USA. 58:719-726.
28. Morrison, L. E., and L. M. Stols. 1993. Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. Biochemistry. 32:3095-3104.
29. Seelig, G., B. Yurke, and E. Winfree. 2005. DNA hybridization catalysts and catalyst circuits. In DNA Computing: 10th International Workshop. Lecture Notes in Computer Science, Vol. 3384. C. Ferretti, G. Mauri, and C. Zandron, editors. Springer, New York. 329-343.
30. Weixlbaumer, A., A. Werner, C. Flamm, E. Westhof, and R. Schroeder. 2004. Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes. Nucleic Acids Res. 32:5126-5133.
31. Gobush, W., H. Yamakawa, W. H. Stockmayer, and W. S. Magee. 1972. Statistical mechanics of wormlike chains. I. Asymptotic behaviour. J. Chem. Phys. 57:2839-2842.
32. Yamakawa, H., and W. H. Stockmayer. 1972. Statistical mechanics of wormlike chain. II. Excluded volume effects. J. Chem. Phys. 57:2843-2854.