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Journal of Nucleic Acids
Volume 2011, Article ID 986820, 7 pages
http://dx.doi.org/10.4061/2011/986820
Research Article

Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

Department of Chemistry and Biochemistry, The University of Mississippi, Coulter Hall, Room 409, MS 38677, USA

Received 15 May 2011; Accepted 19 June 2011

Academic Editor: F. C. Simmel

Copyright © 2011 Yogini P. Bhavsar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Burge, G. N. Parkinson, P. Hazel, A. K. Todd, and S. Neidle, “Quadruplex DNA: sequence, topology and structure,” Nucleic Acids Research, vol. 34, no. 19, pp. 5402–5415, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. M. D. Frank-Kamenetskii and S. M. Mirkin, “Triplex DNA structures,” Annual Review of Biochemistry, vol. 64, pp. 65–95, 1995. View at Google Scholar · View at Scopus
  3. M. S. Han, A. K. R. Lytton-Jean, and C. A. Mirkin, “A gold nanoparticle based approach for screening triplex DNA binders,” Journal of the American Chemical Society, vol. 128, no. 15, pp. 4954–4955, 2006. View at Publisher · View at Google Scholar · View at Scopus
  4. R. M. Wadkins, “Targeting DNA secondary structures,” Current Medicinal Chemistry, vol. 7, no. 1, pp. 1–15, 2000. View at Google Scholar · View at Scopus
  5. C. T. McMurray, “DNA secondary structure: a common and causative factor for expansion in human disease,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 5, pp. 1823–1825, 1999. View at Publisher · View at Google Scholar · View at Scopus
  6. H. J. Lipps and D. Rhodes, “G-quadruplex structures: in vivo evidence and function,” Trends in Cell Biology, vol. 19, no. 8, pp. 414–422, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. H. Moore, P. W. Greenwell, C. P. Liu, N. Arnheim, and T. D. Petes, “Triplet repeats form secondary structures that escape DNA repair in yeast,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 4, pp. 1504–1509, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Nambiar, G. Goldsmith, B. T. Moorthy et al., “Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma,” Nucleic Acids Research, vol. 39, pp. 936–948, 2011. View at Google Scholar
  9. D. B. Davies, V. I. Pahomov, and A. N. Veselkov, “NMR determination of the conformational and drug binding properties of the DNA heptamer d(GpCpGpApApGpC) in aqueous solution,” Nucleic Acids Research, vol. 25, no. 22, pp. 4523–4531, 1997. View at Google Scholar · View at Scopus
  10. W. Mäueler, G. Bassili, C. Epplen, H. G. Keyl, and J. T. Epplen, “Protein binding to simple repetitive sequences depends on DNA secondary structure(s),” Chromosome Research, vol. 7, no. 3, pp. 163–166, 1999. View at Publisher · View at Google Scholar · View at Scopus
  11. T. A. Brooks and L. H. Hurley, “Targeting MYC expression through G-quadruplexes,” Genes Cancer, vol. 1, pp. 641–649, 2010. View at Google Scholar
  12. T. A. Brooks, S. Kendrick, and L. Hurley, “Making sense of G-quadruplex and i-motif functions in oncogene promoters,” FEBS Journal, vol. 277, no. 17, pp. 3459–3469, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. M. Kimoto, T. Mitsui, S. Yokoyama, and I. Hirao, “A unique fluorescent base analogue for the expansion of the genetic alphabet,” Journal of the American Chemical Society, vol. 132, no. 14, pp. 4988–4989, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. M. J. Rist and J. P. Marino, “Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions,” Current Organic Chemistry, vol. 6, no. 9, pp. 775–793, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. P. Sandin, L. M. Wilhelmsson, P. Lincoln, V. E. Powers, T. Brown, and B. Albinsson, “Fluorescent properties of DNA base analogue tC upon incorporation into DNA—negligible influence of neighbouring bases on fluorescence quantum yield,” Nucleic Acids Research, vol. 33, no. 16, pp. 5019–5025, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. S. J. O. Hardman and K. C. Thompson, “Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids,” Biochemistry, vol. 45, no. 30, pp. 9145–9155, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. X. Zhang and R. M. Wadkins, “DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies,” Biophysical Journal, vol. 96, no. 5, pp. 1884–1891, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. S. Preus, K. Kilså, L. M. Wilhelmsson, and B. Albinsson, “Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family,” Physical Chemistry Chemical Physics, vol. 12, no. 31, pp. 8881–8892, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. P. Sandin, K. Börjesson, H. Li et al., “Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue,” Nucleic Acids Research, vol. 36, no. 1, pp. 157–167, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. L. M. Wilhelmsson, “Fluorescent nucleic acid base analogues,” Quarterly Reviews of Biophysics, vol. 43, no. 2, pp. 159–183, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. M. S. Z. Horwitz, “Transcription regulation in vitro by an E. coli promoter containing a DNA cruciform in the -35 region,” Nucleic Acids Research, vol. 17, no. 14, pp. 5537–5545, 1989. View at Google Scholar · View at Scopus
  22. D. M. J. Lilley, D. Chen, and R. P. Bowater, “DNA supercoiling and transcription: topological coupling of promoters,” Quarterly Reviews of Biophysics, vol. 29, no. 3, pp. 203–225, 1996. View at Google Scholar · View at Scopus
  23. N. P. Johnson, W. A. Baase, and P. H. von Hippel, “Low energy CD of RNA hairpin unveils a loop conformation required for λN antitermination activity,” Journal of Biological Chemistry, vol. 280, no. 37, pp. 32177–32183, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. D. Jose, K. Datta, N. P. Johnson, and P. H. von Hippel, “Spectroscopic studies of position-specific DNA “breathing” fluctuations at replication forks and primer-template junctions,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 11, pp. 4231–4236, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. J. Kypr, I. Kejnovská, D. Renčiuk, and M. Vorlíčková, “Circular dichroism and conformational polymorphism of DNA,” Nucleic Acids Research, vol. 37, no. 6, pp. 1713–1725, 2009. View at Publisher · View at Google Scholar
  26. N. P. Johnson, W. A. Baase, and P. H. von Hippel, “Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 20, pp. 7169–7173, 2005. View at Publisher · View at Google Scholar · View at Scopus