Characterization of PicoGreen interaction with dsDNA and the origin of its fluorescence enhancement upon binding

Biophysical Journal

Volumn 99, Issue 9, 2010, Pages 3010-3019

  Dragan, A I ^a   Casas Finet, J R ^b   Bishop, E S ^b   Strouse, R J ^b   Schenerman, M A ^b   Geddes, C D ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b MEDIMMUNE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77958490248     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.09.012     Document Type: Article

References (31)

1. Ahn, S. J., J. Costa, and J. R. Emanuel. 1996. PicoGreen quantitation of DNA: effective evaluation of samples pre-or post-PCR. Nucleic Acids Res. 24:2623-2625.
2. Schneeberger, C., P. Speiser., R. Zeillinger. 1995. Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain. PCR Methods Appl. 4:234-238.
3. Singer, V. L., L. J. Jones., R. P. Haugland. 1997. Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation. Anal. Biochem. 249:228-238.
4. Zipper, H., H. Brunner., F. Vitzthum. 2004. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 32: e103.
5. Blaheta, R. A., B. Kronenberger., B. H. Markus. 1998. Development of an ultrasensitive in vitro assay to monitor growth of primary cell cultures with reduced mitotic activity. J. Immunol. Methods. 211:159-169.
6. Choi, S. J., and F. C. Szoka. 2000. Fluorometric determination of deoxyribonuclease I activity with PicoGreen. Anal. Biochem. 281:95-97.
7. Dragan, A. I., E. S. Bishop., C. D. Geddes. 2010. Metal-enhanced PicoGreen fluorescence: application for double-stranded DNA quantification. Anal. Biochem. 396:8-12.
8. Murakami, P., and M. T. McCaman. 1999. Quantitation of adenovirus DNA and virus particles with the PicoGreen fluorescent dye. Anal. Biochem. 274:283-288.
9. Noothi, S. K., M. Kombrabail., G. Krishnamoorthy. 2009. Fluorescence characterization of the structural heterogeneity of polytene chromosomes. J. Fluoresc. 20:37-41.
10. Noothi, S. K., M. Kombrabail., B. J. Rao. 2009. Enhanced DNA dynamics due to cationic reagents, topological states of dsDNA and high mobility group box 1 as probed by PicoGreen. FEBS J. 276:541-551.
11. Ikeda, Y., S. Iwakiri, and T. Yoshimori. 2009. Development and characterization of a novel host cell DNA assay using ultra-sensitive fluorescent nucleic acid stain "PicoGreen". J. Pharm. Biomed. Anal. 49:997-1002.
12. Geddes, C. D., and J. R. Lakowicz. 2002. Metal-enhanced fluorescence. J. Fluoresc. 12:121-129.
13. Sobell, H. M., C. C. Tsai., S. G. Gilbert. 1977. Visualization of drugnucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions. J. Mol. Biol. 114:333-365.
14. Reference deleted in proof.
15. Dragan, A. I., R. Carrillo., P. L. Privalov. 2008. Assembling the human IFN-β enhanceosome in solution. J. Mol. Biol. 384:335-348.
16. Lakowicz, J. R. 2006. Principles of Fluorescence Spectroscopy. Springer Science + Business Media, New York.
17. Cosa, G., K. S. Focsaneanu., J. C. Scaiano. 2001. Photophysical properties of fluorescent DNA-dyes bound to single-and doublestranded DNA in aqueous buffered solution. Photochem. Photobiol. 73:585-599.
18. McGhee, J. D., and P. H. von Hippel. 1974. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86:469-489.
19. Dragan, A. I., J. R. Liggins., P. L. Privalov. 2003. The energetics of specific binding of AT-hooks from HMGA1 to target DNA. J. Mol. Biol. 327:393-411.
20. Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179-246.
21. Record, Jr., M. T., C. F. Anderson, and T. M. Lohman. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11:103-178.
22. Record, Jr., M. T., W. Zhang, and C. F. Anderson. 1998. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51:281-353.
23. Crane-Robinson, C., A. I. Dragan, and P. L. Privalov. 2006. The extended arms of DNA-binding domains: a tale of tails. Trends Biochem. Sci. 31:547-552.
24. Dragan, A. I., C. M. Read., P. L. Privalov. 2004. DNA binding and bending by HMG boxes: energetic determinants of specificity. J. Mol. Biol. 343:371-393.
25. Privalov, P. L., A. I. Dragan., C. A. Minetti. 2007. What drives proteins into the major or minor grooves of DNA? J. Mol. Biol. 365:1-9.
26. Lippard, S. J. 1978. Platinum complexes-probes of polynucleotide structure and anti-tumor drugs. Acc. Chem. Res. 11:211-217.
27. Kovacic, R. T., and K. E. van Holde. 1977. Sedimentation of homogeneous double-strand DNA molecules. Biochemistry. 16:1490-1498.
28. 2 duplex: calorimetric and spectroscopic studies. J. Mol. Biol. 271:244-257.
29. Utsuno, K., Y. Maeda, and M. Tsuboi. 1999. How and how much can Hoechst 33258 cause unwinding in a DNA duplex? Chem. Pharm. Bull. (Tokyo). 47:1363-1368.
30. Pjura, P. E., K. Grzeskowiak, and R. E. Dickerson. 1987. Binding of Hoechst 33258 to the minor groove of B-DNA. J. Mol. Biol. 197:257-271.
31. Lakowicz, J. R., and G. Weber. 1973. Quenching of fluorescence by oxygen. A probe for structural fluctuations in macromolecules. Biochemistry. 12:4161-4170.