Configuring robust DNA strand displacement reactions for in situ molecular analyses

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages 3289-3298

  Duose, Dzifa Y ^a   Schweller, Ryan M ^a   Zimak, Jan ^a   Rogers, Arthur R ^a   Hittelman, Walter N ^b   Diehl, Michael R ^a,c  

^a Rice University   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MARKER; FLUORESCENT DYE; OLIGONUCLEOTIDE; PROTEIN; SINGLE STRANDED DNA;

ANIMAL CELL; ARTICLE; CHEMICAL LABELING; DNA PROBE; DNA STRAND DISPLACEMENT REACTION; FLUORESCENCE MICROSCOPY; GENETIC ENGINEERING AND GENE TECHNOLOGY; IN SITU LABELING; INTERACTIONS WITH DNA; MOLECULAR IMAGING; MOLECULAR PROBE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; TISSUE SECTION;

ANIMALS; CHO CELLS; CRICETINAE; CRICETULUS; DNA PROBES; IN SITU HYBRIDIZATION, FLUORESCENCE; KINETICS; MICROSCOPY, FLUORESCENCE; MOLECULAR IMAGING; PROTEINS;

EID: 84860209090     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1209     Document Type: Article

References (26)

1. Stojanovic, M.N., Mitchell, T.E. and Stefanovic, D. (2002) Deoxyribozyme-based logic gates. J. Am. Chem. Soc., 124, 3555-3561. (Pubitemid 34407878)
2. Seelig, G., Soloveichik, D., Zhang, D.Y. and Winfree, E. (2006) Enzyme-free nucleic acid logic circuits. Science, 314, 1585-1588. (Pubitemid 44907149)
3. Hagiya, M., Yaegashi, S. and Takahashi, K. (2006) Computing with hairpins and secondary structures of DNA. Nanotechnol. Science Comput., 293-308.
4. Dirks, R.M. and Pierce, N.A. (2004) Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci., 101, 15275-15278. (Pubitemid 39441531)
5. Lubrich, D., Green, S.J. and Turberfield, A.J. (2009) Kinetically controlled self-assembly of DNA oligomers. J. Am. Chem. Soc., 131, 2422-2423.
6. Goodman, R.P., Heilemann, M., Doose, S., Erben, C.M., Kapanidis, A.N. and Turberfield, A.J. (2008) Roconfigurable, braced, three-dimensional DNA nanostructures. Nat. Nanotechnol., 3, 93-96. (Pubitemid 351225403)
7. Zhang, D.Y. and Seelig, G. (2011) Dynamic DNA nanotechnology using strand displacement reactions. Nat. Chem., 3, 103-113.
8. Zhang, D.Y. (2011) Cooperative hybridization of oligonucleotides. J. Am. Chem. Soc., 133, 1077-1086.
9. Zhang, D.Y. and Winfree, E. (2010) Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic Acids Res., 38, 4182-4197.
10. Qian, L. and Winfree, E. (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science, 332, 1196-1201.
11. Yurke, B., Mills, A.P. and Cheng, S.L. (1999) DNA implementation of addition in which the input strands are separate from the operator strands. Biosystems, 52, 165-174. (Pubitemid 29518360)
12. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression. Nature, 429, 423-429. (Pubitemid 38715134)
13. Duose, D.Y., Schweller, R.M., Hittelman, W.N. and Diehl, M.R. (2010) Multiplexed and reiterative fluorescence labeling via DNA circuitry. Bioconjug. Chem., 21, 2327-2331.
14. Venkataraman, S., Dirks, R.M., Ueda, C.T. and Pierce, N.A. (2010) Selective cell death mediated by small conditional RNAs. Proc. Natl Acad. Sci., 107, 16777-16782.
15. Choi, H.M.T., Chang, J.Y., Trinh, L.A., Padilla, J.E., Fraser, S.E. and Pierce, N.A. (2010) Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol., 28, 1208-1212.
16. Zhang, D.Y. and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc., 131, 17303-17314.
17. Feng, B., Frykholm, K., Norde, B. and Westerlund, F. (2010) DNA strand exchange catalyzed by molecular crowding in PEG solutions. Chem. Commun., 46, 8231-8233.
18. Moll, J.R., Ruvinov, S.B., Pastan, I. and Vinson, C. (2001) Designed heterodimerizing leucine zippers with a range of pIs and stabilities up to 10(-15) M. Protein Sci., 10, 649-655. (Pubitemid 32221153)
19. Schweller, R.M., Constantinou, P.E., Frankel, N.W., Narayan, P. and Diehl, M.R. (2008) Design of DNA-conjugated polypeptide-based capture probes for the anchoring of proteins to DNA matrices. Bioconjug. Chem., 19, 2304-2307.
20. Zhang, D.Y., Turberfield, A.J., Yurke, B. and Winfree, E. (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science, 318, 1121-1125. (Pubitemid 350134891)
21. Rouillard, J.M., Zuker, M. and Gulari, E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062. (Pubitemid 37441764)
22. Lilley, D.M.J. (2000) Structures of helical junctions in nucleic acids. Q. Rev. Biophys., 33, 109-159.
23. Karymov, M., Douglas, D., Sankey, O.F. and Lyubchenko, Y.L. (2005) Holliday junction dynamics and branch migration: single-molecule analysis. Proc. Natl Acad. Sci., 102, 8186-8191. (Pubitemid 40800064)
24. Zadeh, J.N., Steenberg, C.D., Bois, J.S., Wolfe, B.R., Pierce, M.B., Khan, A.R., Dirks, R.M. and Pierce, N.A. (2011) NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem., 32, 170-173.
25. Dirks, R.M., Bois, J.S., Schaeffer, J.M., Winfree, E. and Pierce, N.A. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev., 49, 65-88. (Pubitemid 46351352)
26. Friedman, L.J., Chung, J. and Gelles, J. (2006) Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. Biophys. J., 91, 1023-1031. (Pubitemid 44161935)