Optimizing the specificity of nucleic acid hybridization (original) (raw)

References

  1. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).
    Article CAS Google Scholar
  2. Saiki, R. K. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491 (1988).
    Article CAS Google Scholar
  3. Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).
    Article CAS Google Scholar
  4. Gunderson, K. L., Steemers, F. J., Lee, G., Mendoza, L. G. & Chee, M. S. A genome-wide scalable SNP genotyping assay using microarray technology. Nature Genet. 37, 549–554 (2005).
    Article CAS Google Scholar
  5. Koltai, H. & Weingarten-Baror, C. Specificity of DNA microarray hybridization: characterization, effectors, and approaches for data correction. Nucleic Acids Res. 36, 2395–2405 (2008).
    Article CAS Google Scholar
  6. DeLong, E. F., Wickham, G. S. & Pace, N. R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243, 1360–1363 (1989).
    Article CAS Google Scholar
  7. Amann, R. I., Krumholz, L. & Stahl, D. A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172, 762–770 (1990).
    Article CAS Google Scholar
  8. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010).
    Article CAS Google Scholar
  9. Rothemund, P. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
    Article CAS Google Scholar
  10. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).
    Article CAS Google Scholar
  11. Aldaye, F. A., Palmer, A. L. & Sleiman, H. F. Assembling materials with DNA as the guide. Science 321, 1795–1799 (2008).
    Article CAS Google Scholar
  12. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318–322 (2008).
    Article CAS Google Scholar
  13. Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand displacement reactions. Nature Chem. 3, 103–113 (2011).
    Article CAS Google Scholar
  14. Tyagi, S. & Kramer, F. R. Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnol. 14, 303–308 (1996).
    Article CAS Google Scholar
  15. Tyagi, S., Bratu, D. P. & Kramer, F. R. Multicolor molecular beacons for allele discrimination. Nature Biotechnol. 16, 49–53 (1998).
    Article CAS Google Scholar
  16. Tyagi, S. Imaging intracellular RNA distribution and dynamics in living cells. Nature Methods 6, 331–338 (2009).
    Article CAS Google Scholar
  17. Bonnet, G., Tyagi, S., Libchaber, A. & Kramer, F. R. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl Acad. Sci. USA 96, 6171–6176 (1999).
    Article CAS Google Scholar
  18. Tsourkas, A., Behlke, M. A., Rose, S. D. & Bao, G. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 31, 1319–1330 (2003).
    Article CAS Google Scholar
  19. Xiao, Y. et al. Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. Angew. Chem. Int. Ed. 48, 4354–4358 (2009).
    Article CAS Google Scholar
  20. Kolpashchikov, D. M. A binary DNA probe for highly specific nucleic acid recognition. J. Am. Chem. Soc. 128, 10625–10628 (2006).
    Article CAS Google Scholar
  21. Dave N. & Liu, J. Fast molecular beacon hybridization in organic solvents with improved target specificity. J. Phys. Chem. B 114, 15694–15699 (2010).
    Article CAS Google Scholar
  22. SantaLucia, J. & Hicks, D. The thermodynamics of DNA structural motifs. Ann. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).
    Article CAS Google Scholar
  23. Peyret, N. Prediction of Nucleic Acid Hybridization: Parameters and Algorithms. Doctoral thesis, Wayne State University (2000).
  24. Tan, Z. J. & Chen, S. J. Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys. J. 90, 1175–1190 (2006).
    Article CAS Google Scholar
  25. Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).
    Article CAS Google Scholar
  26. Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009).
    Article CAS Google Scholar
  27. Zhang, D. Y., Turberfield, A. J., Yurke, B. & Winfree, E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121–1125 (2007).
    Article CAS Google Scholar
  28. He, G., Rapireddy, S., Bahal, R., Sahu, B. & Ly, D. H. Strand invasion of extended, mixed-sequence B-DNA by γPNAs. J. Am. Chem. Soc. 131, 12088–12090 (2009).
    Article CAS Google Scholar
  29. Petersen, M. & Wengel, J. LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol. 21, 74–81 (2003).
    Article CAS Google Scholar
  30. Bommarito, S., Peyret, N. & SantaLucia, J. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929–1934 (2000).
    Article CAS Google Scholar
  31. Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E. & Pierce, N. A. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev. 49, 65–88 (2007).
    Article Google Scholar
  32. Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic Acids Res. 38, 4182–4197 (2010).
    Article CAS Google Scholar
  33. Temsamani, J., Kubert, M. & Agrawal, S. Sequence identity of the _n_–1 product of a synthetic oligonucleotide. Nucleic Acids Res. 23, 1841–1844 (1995).
    Article CAS Google Scholar
  34. Marras, S. A., Kramer, F. R. & Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122 (2002).
    Article Google Scholar
  35. Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834–838 (2005).
    Article CAS Google Scholar
  36. Li, Q., Luan, G., Guo, Q. & Liang, J. A new class of homogeneous nucleic acid probe based on specific displacement hybridization. Nucleic Acids Res. 30, e5 (2002).
    Article Google Scholar
  37. Subramanian, H. K. K., Chakraborty, B., Sha, R. & Seeman, N. C. The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami. Nano Lett. 11, 910–913 (2010).
    Article Google Scholar
  38. Gao, Y., Wolf, L. K. & Georgiadis, R. M. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res. 34, 3370–3377 (2006).
    Article CAS Google Scholar
  39. Kim, S. & Misra A. SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9, 289–320 (2007).
    Article CAS Google Scholar
  40. Lizardi, P. M. et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19, 225–232 (1998).
    Article CAS Google Scholar
  41. Isaacs, F. J., et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnol. 22, 841–847 (2004).
    Article CAS Google Scholar
  42. Venkataraman, S., Dirks, R. M., Ueda, C. T. & Pierce, N. Selective cell death mediated by small conditional RNAs. Proc. Natl Acad. Sci. USA 107, 16777–16782 (2010).
    Article CAS Google Scholar

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