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Optical Detection of Thymine Dinucleoside Monophosphate and Its cis-syn Photodimer by Inorganic Nanoparticles

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Abstract

The Watson-Crick DNA double helix is an averaged ideal of multitudinous natural sequence-directed local structural deviations. By effectively derailing normal cellular physiological processes, damaged bases can induce noncanonical irregularities in the local structure of DNA if not efficiently repaired. Pyrimidine bases, especially thymine, are prone to dimerization when exposed to ultraviolet light. A [2 + 2] photocyclo-addition between adjacent thymine bases predominantly produces the cis-syn photodimer. These lesions, implicated in skin cancer, bend DNA by ∼30° due to their structural and conformational changes. Such changes in molecular properties can be detected by differential quenching of CdS nanoparticle luminescence and by surface-enhanced Raman scattering spectroscopy on metal nanoparticle substrates.

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REFERENCES

  1. P. Catasti, X. Chen, S. V. S. Mariappan, E. M. Bradbury, and G. Gupta (1999). DNA repeats in the human genome. Genetica (The Hague) 106, 15-36.

    Google Scholar 

  2. X. Chen, S. V. S. Mariappan, P. Catasti, R. Ratliff, R. K. Moyzis, A. Laayoun, S. S. Smith, E. M. Bradbury, and G. Gupta (1995). Hairpins are formed by the single DNA strands of the fragile-X triplet repeats-Structure and biological implications. Proc. Natl. Acad. Sci. U.S.A. 92, 5199-5203.

    Google Scholar 

  3. R. D. Wells and Eds. C. Harvey (Eds.) (1988). Unusual DNA Structures, Springer-Verlag, New York.

    Google Scholar 

  4. R. R. Sinden (1994). DNA Structure and Function, Academic Press, San Diego, CA.

    Google Scholar 

  5. A. P. Wolffe and H. R. Drew (1995). In Eds. C. R. Elgin (Ed.), Chromatin Structure and Gene Expression, IRL, Oxford, pp. 27-48.

    Google Scholar 

  6. C. R. Calladine and H. R. Drew (1997). Understanding DNA, Academic Press, San Diego, CA.

    Google Scholar 

  7. H. Park, K. J. Zhang, Y. J. Ren, S. Nadji, N. Sinha, J. S. Taylor, C. H. Kang (2002). Crystal structure of a decamer containing a cis-syn thymine dimer. Proc. Natl. Acad. Sci. U.S.A. 99, 15965-15970.

    Google Scholar 

  8. S. Y. Wang (1976). Photochemistry and Photobiology of Nucleic Acids: Vol. I, Chemistry, Academic Press, New York.

    Google Scholar 

  9. T. Douki, M. Court, F. O. Sauvaigo, and J. Cadet (2000). Formation of the main UV-induced thymine dimeric lesions within isolated and cellular DNA as measured by high performance liquid chromatography-tandem mass spectrometry. J. Biol. Chem. 275, 11678-11685.

    Google Scholar 

  10. I. Husain, J. Griffith, and A. Sancar (1988). Thymine dimers bend DNA. Proc. Natl. Acad. Sci. U.S.A. 85, 2558-2562.

    Google Scholar 

  11. J. J. Storhoff, R. Elghanian, R. C. Mucic, C. A. Mirkin, and R. L. Letsinger (1998). One pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle Probes. J. Am. Chem. Soc. 120, 1959-1964.

    Google Scholar 

  12. C. J. Murphy and R. Mahtab (2000). Detection of unusual DNA structures with nanoparticles. Proc. SPIE 3924, 10-16.

    Google Scholar 

  13. R. Mahtab, J. P. Rogers, and C. J. Murphy (1995). Protein-sized quantum-dot luminescence can distinguish between “Straight,” “Bent,” and “Kinked” oligonucleotides. J. Am. Chem. Soc. 117, 9099-9100.

    Google Scholar 

  14. R. Mahtab, J. P. Rogers, C. P. Singleton, and C. J. Murphy (1996). Preferential adsorption of a “Kinked” DNA to a neutral curved surface: Comparisons to and implications for nonspecific DNA-protein Interactions. J. Am. Chem. Soc. 118, 7028-7032.

    Google Scholar 

  15. C. J. Murphy, E. B. Brauns, and L. Gearheart (1997). Quantum dots as inorganic DNA-binding proteins. Mat. Res. Soc. Symp. Proc. 452, 597-600.

    Google Scholar 

  16. R. Mahtab, H. H. Harden, and C. J. Murphy (2000). Temperature-and salt-dependent binding of long DNA to protein-sized quantum dots: Thermodynamics of “Inorganic Protein”-DNA interactions. J. Am. Chem. Soc. 122, 14-17.

    Google Scholar 

  17. L. Gearheart, K. K. Caswell, and C. J. Murphy (2001). Recognition of hypermethylated triplet repeats in vitro by cationic nanoparticles. J. Biomed. Opt. 6, 111-115.

    Google Scholar 

  18. K. Kneipp, H. Kneipp, I. Itzkan, R. R. Dasari, and M. S. Feld (1999). Ultrasensitive chemical analysis by Raman spectroscopy. Chem. Rev. 99, 2957-2976.

    Google Scholar 

  19. W. E. Doering and S. Nie (2002). Single-molecule and single-nanoparticle SERS: Examining the roles of surface active sites and chemical enhancement. J. Phys. Chem. B 106, 311-317.

    Google Scholar 

  20. J. A. Creighton (1983). Surface Raman electromagnetic enhancement factors for molecules at the surface of small isolated metal spheres-The determination of adsorbate orientation from SERS relative intensities. Surf. Sci. 124, 209-219.

    Google Scholar 

  21. A. Campion and P. Kambhampati (1998). Surface-enhanced Raman scattering. Chem. Soc. Rev. 27, 241-250.

    Google Scholar 

  22. R. L. Garrell (1989). Surface-enhanced Raman-spectroscopy. Anal. Chem. 61, 401A-411A.

    Google Scholar 

  23. M. Moskovits (1985). Surface-enhanced spectroscopy. Rev. Mod. Phys. 57, 783-826.

    Google Scholar 

  24. A. M. Michaels, J. Nirmal, and L. E. Brus (1999). Surface enhanced Raman spectroscopy of individual rhodamine 6G molecules on large Ag nanocrystals. J. Am. Chem. Soc. 121, 9932-9939.

    Google Scholar 

  25. K. Kneipp, H. Kneipp, R. Manoharan, I. Itzkan, R. R. Dasari, and M. S. Feld (1998). Surface-enhanced Raman scattering (SERS)-A new tool for single molecule detection and identification. Bioimaging 6, 104-110.

    Google Scholar 

  26. K. Kneipp, Y. Wang, H. Kneipp, L. T. Perelman, I. Itzkan, R. R. Dasari, and M. S. Feld (1997). Single molecule detection using surface-enhanced Raman scattering (SERS). Phys. Rev. Lett. 78, 1667-1670.

    Google Scholar 

  27. K. Kneipp, H. Kneipp, V. B. Kartha, R. Manoharan, G. Deinum, I. Itzkan, R. R. Dasari, and M. S. Feld, (1998). Detection and identification of a single DNA base molecule using surface-enhanced Raman scattering (SERS). Phys. Rev. E 57, R6281-R6284.

    Google Scholar 

  28. S. M. Nie and S. R. Emory (1997). Probing single molecules and single nanoparticles by surface-enhanced Raman scattering. Science 275, 1102-1106.

    Google Scholar 

  29. L. A. Gearheart, H. J. Ploehn, and C. J. Murphy (2001). Oligonucleotide adsorption to gold nanoparticles: A surface-enhanced Raman spectroscopy study of intrinsically bent DNA. J. Phys. Chem. B 105, 12609-12615.

    Google Scholar 

  30. J. E. Yager and C. D. Yue (1988). Evaluation of the xenon arc lamp as a light source for aquatic photodegradation studies-Comparison with natural sunlight. Environ. Toxicol. Chem. 7, 1003-1011.

    Google Scholar 

  31. L.-S. Kan, L. Voituriez, and J. Cadet (1988). Nuclear magnetic-resonance studies of cis-syn, trans-syn, and 6-4 photodimers of thymidylyl(3'-5')thymidine monophosphate and cis-syn photodimers of thymidylyl(3'-5')thymidine cyanoethyl phosphotriester. Biochemistry 27, 5796-5803.

    Google Scholar 

  32. G. D. Fasman (1996). Circular Dichroism and the Conformational Analysis of Biomolecules, Plenum, New York.

    Google Scholar 

  33. S. Schneider, P. Halbig, H. Grau, and U. Nickel (1994). Reproducible preparation of silver sols with uniform particle size for application in surface-enhanced Raman spectroscopy. Photochem. Photobiol. 60, 605-610.

    Google Scholar 

  34. P. Atkins (1994). Physical Chemistry, 5th Ed., Freeman, New York.

    Google Scholar 

  35. V. K. Rastogi, C. Singh, V. Jain, and M. A. Palafox (2000). FTIR and FT-Raman spectra of 5-methyluracil (thymine). J. Raman Spectrosc. 31, 1005-1012.

    Google Scholar 

  36. C. Otto, T. J. J. van den Tweel, F. F. M. de Mul, and J. Greve (1986). Surface-enhanced Raman-spectroscopy of DNA bases. J. Raman Spectrosc. 17, 289-298.

    Google Scholar 

  37. E. Koglin, J. M. Sequaris, J. C. Fritz, and P. Valenta (1984). Surface-enhanced Raman-scattering (SERS) of nucleic-acid bases adsorbed on silver colloids. J. Mol. Struct. 114, 219-223.

    Google Scholar 

  38. R. Aroca and R. Bujalski (1999). Surface enhanced vibrational spectra of thymine. Vibrational Spectrosc. 19, 11-21.

    Google Scholar 

  39. F. R. Dollish, W. G. Fateley, and F. F. Bentley (1974). Characteristic Raman Frequencies of Organic Compounds, Wiley, New York.

    Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, Columbia, South Carolina, 29208

    K. K. Caswell & Catherine J. Murphy

  2. Department of Physical Sciences, South Carolina State University, Orangeburg, South Carolina, 29117

    Rahina Mahtab

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  1. K. K. Caswell
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  2. Rahina Mahtab
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  3. Catherine J. Murphy
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Correspondence to Catherine J. Murphy.

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Caswell, K.K., Mahtab, R. & Murphy, C.J. Optical Detection of Thymine Dinucleoside Monophosphate and Its cis-syn Photodimer by Inorganic Nanoparticles. Journal of Fluorescence 14, 407–415 (2004). https://doi.org/10.1023/B:JOFL.0000031822.12344.84

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