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Intrinsic DNA fluorescence

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The term intrinsic DNA fluorescence refers to the fluorescence emitted directly by DNA when it absorbs ultraviolet (UV) radiation. It contrasts to that stemming from labels that are attached to DNA strands, widely used in biological applications. The intrinsic DNA fluorescence was discovered in the 1960s by studying nucleic acids in frozen media.[1] Since the beginning of the 21st century, the much weaker emission of nucleic acids in fluid solutions is being studied in room temperature by means sophisticated spectroscopic techniques using as UV source femtosecond laser pulses and following the evolution of the emitted light from femtoseconds to nanoseconds. [2][3][4][5][6][7] Such studies bring information about the relaxation of the electronic excited states[8] and, thus, contribute to understanding the very first steps of a complex series of events triggered by UV radiation, ultimately leading to DNA damage.[9] Moreover, the knowledge of the fundamental processes underlying the DNA fluorescence paves the way for the development of label-free biosensors.[10][11]

Conditions for measuring the intrinsic DNA fluorescence

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Due to the weak intensity of the intrinsic DNA fluorescence, specific cautions are necessary in order to perform correct measurements and obtain reliable results.[12] A first requirement concerns the purity of both the DNA samples and that of the chemicals and the water used to the preparation of the buffered solutions. A second requirement is associated with the DNA damage provoked by the exciting UV light which alters its fluorescence.[13] Therefore, their generation during the experiment may alter the emission spectra. In order to overcome these difficulties, continuous stirring of the solution is needed. For measurements using laser excitation, the circulation of the DNA solution by means of a peristaltic pump is recommended.

Spectral shapes and quantum yields

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The fluorescence of all DNA systems in neutral aqueous solution peaks in the near ultraviolet (300-400 nm) when excited around 260 nm. In addition, a long tail, extending all over the visible domain is present in the fluorescence spectrum. The associated quantum yields Φ, that is the number of emitted photons over the number of absorbed photons, are typically in the range of 10-4-10-3. The highest values are encountered for G-quadruplexes.[14]

A limited number of measurements were also performed upon UVA excitation (330 nm), where DNA single and double strands, but not their monomeric units, absorb weakly.[15] The UVA-induced fluorescence peaks at longer wavelengths (415-430 nm) and the corresponding Φ values are at least one order of magnitude higher compared to those determined with excitation around 260 nm.[16]

Time-resolved studies, combined to theoretical calculations,[17][18] showed that the fluorescence spectrum of DNA multimers (containing more than one nucleobase) is the envelope of multiple components, arising from the electronic coupling between the close-lying nucleobases.[19] Their relative importance depends on a series of factors, such as the base sequence, the secondary structure, the viscosity of the solution or, in the case of G-Quadruplexes, the metal ions in their central cavity.[20][21][22]

Applications

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The utilization of the intrinsic fluorescence of nucleic acids for sensing purposes started to be scrutinized just in 2019. The possibility of detecting target DNA[23] or Pb2+ ions,[24] the screening of a large number of sequences[25] or the authentication of COVID-19 vaccines[26] have been explored. Moreover, the possibility of detecting the DNA damage by probing its fluorescence at short wavelengths (300 nm) has been discussed.[27] Due to their modulable structure, G-quadruplexes, are particularly promising for the development of label-free and dye-free biosensors.[28]

Secondary sources

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Scientific reviews and accounts

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  • Improta, R.; Santoro, F.; Blancafort, L. (2016) Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chemical Reviews, 116 (6), 3540-3593.[29]
  • Markovitsi, D. (2016) UV-induced DNA Damage: The Role of Electronic Excited States. Photochemistry and Photobiology-Invited Review. 92, 45-51.[30]
  • Gustavsson, T.; Markovitsi, D. (2021). Fundamentals of the Intrinsic DNA Fluorescence. Accounts of Chemical Research. 54 (5), 1226-1235. [31]
  • Martinez-Fernandez, L.; Santoro, F.; Improta, R. (2022) Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies. Accounts of Chemical Research.55 (15), 2077-2087[32]
  • Markovitsi, D. (2024) Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors. Photochemistry and Photobiology-Invited Review. 2024, 100 (2), 262–274[33]
  • Markovitsi, D. On the Use of the Intrinsic DNA Fluorescence for Monitoring its Damage - A Contribution from Fundamental Studies. ACS Omega (Review)[34]

Book chapters

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  • Markovitsi, D.; Gustavsson, T. Energy flow in DNA duplexes. In Energy Transfer Dynamics in Biomaterial Systems Burghardt, I., May, V., Micha, D. A., Bittner, E. R. Eds.; Springer Ser. Chem. Phys.,, Vol. 93; Springer, Heidelberg/Berlin, 2009; pp 127-142.[35]
  • Markovitsi, D.; Gustavsson, T.; Banyasz, A. DNA Fluorescence. In CRC Handbook of Organic Photochemistry and Photobiology, Chapter 42. Griesbeck, A., Ghetti, F., Oelgemoeller, M. Eds.; Taylor and Francis, 2012; pp 1057-1079 (ISBN: 9780429100253).[36]
  • Changenet-Barret, P.; Hua, Y.; Markovitsi, D. Electronic excitations in guanine quadruplexes. In Photoinduced Phenomena in Nucleic Acids II, Barbati, M., Borin, A. C., Ulrich, S. Eds.; Top. Curr. Chem., Vol. 356; Springer Nature, 2015; pp 183–202[37]

References

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  1. ^ Eisinger, J. (1966). "Excimer fluorescence of dinucleotides, polynucleotides and DNA". Proc. Natl. Acad. Sci. USA. 55 (5): 1015–1020. Bibcode:1966PNAS...55.1015E. doi:10.1073/pnas.55.5.1015. PMC 224269. PMID 5225506.
  2. ^ Peon, J. (2001). "DNA/RNA nucleotides and nucleosides: direct measurement of excited-state lifetimes by femtosecond fluorescence up-conversion". Chem. Phys. Lett. 348 (3–4): 255–262. Bibcode:2001CPL...348..255P. doi:10.1016/S0009-2614(01)01128-9.
  3. ^ Kwok, W-M. (2006). "Femtosecond time- and wavelength-resolved fluorescence and absorption study of the excited states of adenosine and an adenine oligomer". J. Am. Chem. Soc. 128 (36): 11894–12705. doi:10.1021/ja0622002. PMID 16953630.
  4. ^ Schwalb, N.K. (2008). "Base sequence and higher-order structure induce the complex excited-state dynamics in DNA". Science. 322 (5899): 243–245. Bibcode:2008Sci...322..243S. doi:10.1126/science.1161651. PMID 18845751.
  5. ^ Vaya, I. (2010). "Fluorescence of natural DNA: from the femtosecond to the nanosecond time-scales". J. Am. Chem. Soc. 132 (34): 11834–11835. Bibcode:2010JAChS.13211834V. doi:10.1021/ja102800r. PMID 20698570.
  6. ^ Wang, D.H. (2022). "Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy". Photochem. Photobiol. 22 (5): 1008–1016. doi:10.1111/php.13612. PMID 35203108.
  7. ^ Gustavsson, T. (2023). "The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes" (PDF). J. Phys. Chem. Lett. 14 (8): 2141–2147. doi:10.1021/acs.jpclett.2c03884. PMID 36802626.
  8. ^ Markovitsi, D. (2016). "UV-induced DNA Damage: The Role of Electronic Excited States". Photochem. Photobiol. 92 (1): 45–51. doi:10.1111/php.12533. PMID 26436855.
  9. ^ Yu, Z.W. (2024). "Ultraviolet (UV) radiation: a double-edged sword in cancer development and therapy". Molecular Biomedicine. 5 (1): 49. doi:10.1186/s43556-024-00209-8. PMC 11486887. PMID 39417901.
  10. ^ Xiang, X (2019). "Label-free and dye-free detection of target DNA based on intrinsic fluorescence of the (3+1) interlocked bimolecular G-quadruplexes". Sens. Actuators B Chem. 290 (290): 68–72. Bibcode:2019SeAcB.290...68X. doi:10.1016/j.snb.2019.03.111.
  11. ^ Lopez, A. (2022). "Probing metal-dependent G-quadruplexes using the intrinsic fluorescence of DNA". Chem. Comm. 58 (73): 10225–10228. doi:10.1039/d2cc03967b. PMID 36001027.
  12. ^ Markovitsi, D. (2006). "UVB/UVC induced processes in model DNA helices studied by time-resolved spectroscopy: pitfalls and tricks". J. Photochem. Photobiol. A-Chem. 183 (1–2): 1–8. Bibcode:2006JPPA..183....1M. doi:10.1016/j.jphotochem.2006.05.029.
  13. ^ Carroll, G.T. (2023). "Intrinsic fluorescence of UV-irradiated DNA". J. Photochem. Photobiol. A: Chem. 437: 114484. Bibcode:2023JPPA..43714484C. doi:10.1016/j.jphotochem.2022.114484.
  14. ^ Gustavsson; T. (2021). "Fundamentals of the Intrinsic DNA Fluorescence" (PDF). Acc. Chem. Res. 54 (5): 1226–1235. doi:10.1021/acs.accounts.0c00603. PMID 33587613.
  15. ^ Mouret, S. (2010). "UVA-induced cyclobutane pyrimidine dimers in DNA: a direct photochemical mechanism?" (PDF). Org. Biomol. Chem. 8 (7): 1706–1711. doi:10.1039/b924712b. PMID 20237685.
  16. ^ Banyasz, A. (2011). "Base-pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA" (PDF). J. Am. Chem. Soc. 133 (14): 5163–5165. Bibcode:2011JAChS.133.5163B. doi:10.1021/ja110879m. PMID 21417388.
  17. ^ Spata, V.A. (2016). "Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides". J. Chem. Phys. Lett. 7 (6): 976–984. doi:10.1021/acs.jpclett.5b02756. PMID 26911276.
  18. ^ Martinez-Fernandez, L. (2022). "Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies". Acc. Chem. Res. 55 (15): 2077–2087. doi:10.1021/acs.accounts.2c00256. PMID 35833758.
  19. ^ Gustavsson; T. (2021). "Fundamentals of the Intrinsic DNA Fluorescence" (PDF). Acc. Chem. Res. 54 (5): 1226–1235. doi:10.1021/acs.accounts.0c00603. PMID 33587613.
  20. ^ Dao, N.T. (2011). "Following G-quadruplex formation by its intrinsic fluorescence". FEBS Letters. 585 (24): 3969–3977. Bibcode:2011FEBSL.585.3969D. doi:10.1016/j.febslet.2011.11.004. hdl:10356/98618. PMID 22079665.
  21. ^ Ma, M.S. (2019). "Real-time Monitoring Excitation Dynamics of Human Telomeric Guanine Quadruplexes: Effect of Folding Topology, Metal Cation, and Confinement by Nanocavity Water Pool". J. Phys. Chem. Lett. 10 (24): 7577–7585. doi:10.1021/acs.jpclett.9b02932. PMID 31769690.
  22. ^ Markovitsi, D. (2024). "10.1021/acsomega.4c02256". ACS Omega. 9 (25): 26826–26837. doi:10.1021/acsomega.4c02256. PMC 11209687. PMID 38947837.
  23. ^ Xiang, X (2019). "Label-free and dye-free detection of target DNA based on intrinsic fluorescence of the (3+1) interlocked bimolecular G-quadruplexes". Sens. Actuators B Chem. 290 (290): 68–72. Bibcode:2019SeAcB.290...68X. doi:10.1016/j.snb.2019.03.111.
  24. ^ Lopez, A. (2022). "Probing metal-dependent G-quadruplexes using the intrinsic fluorescence of DNA". Chem. Comm. 58 (73): 10225–10228. doi:10.1039/d2cc03967b. PMID 36001027.
  25. ^ Zuffo, M. (2020). "Harnessing intrinsic fluorescence for typing of secondary structures of DNA". Nucl. AC. Res. 48 (11): e61. doi:10.1093/nar/gkaa257. PMC 7293009. PMID 32313962.
  26. ^ Assi, S. (2023). "Authentication of Covid-19 Vaccines Using Synchronous Fluorescence Spectroscopy". J. Fluoresc. 33 (3): 1165–1174. doi:10.1007/s10895-022-03136-5. PMC 9825072. PMID 36609659.
  27. ^ Markovitsi, D. (2024). "10.1021/acsomega.4c02256". ACS Omega. 9 (25): 26826–26837. doi:10.1021/acsomega.4c02256. PMC 11209687. PMID 38947837.
  28. ^ Markovitsi, D. (2024). "Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors". Photochem. Photobiol. 100 (2): 262–274. doi:10.1111/php.13826. PMID 37365765.
  29. ^ Improta, Roberto; Santoro, Fabrizio; Blancafort, Lluís (2016). "Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases". Chemical Reviews. 116 (6): 3540–3593. doi:10.1021/acs.chemrev.5b00444. PMID 26928320.
  30. ^ Markovitsi, Dimitra (2016). "UV-inducedDNADamage: The Role of Electronic Excited States". Photochemistry and Photobiology. 92 (1): 45–51. doi:10.1111/php.12533. PMID 26436855.
  31. ^ Gustavsson, Thomas; Markovitsi, Dimitra (2021). "Fundamentals of the Intrinsic DNA Fluorescence". Accounts of Chemical Research. 54 (5): 1226–1235. doi:10.1021/acs.accounts.0c00603. PMID 33587613.
  32. ^ Martínez Fernández, Lara; Santoro, Fabrizio; Improta, Roberto (2022). "Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies". Accounts of Chemical Research. 55 (15): 2077–2087. doi:10.1021/acs.accounts.2c00256. PMID 35833758.
  33. ^ Markovitsi, Dimitra (2024). "Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors". Photochemistry and Photobiology. 100 (2): 262–274. doi:10.1111/php.13826. PMID 37365765.
  34. ^ Markovitsi, Dimitra (2024). "On the Use of the Intrinsic DNA Fluorescence for Monitoring Its Damage: A Contribution from Fundamental Studies". ACS Omega. 9 (25): 26826–26837. doi:10.1021/acsomega.4c02256. PMC 11209687. PMID 38947837.
  35. ^ Markovitsi, Dimitra; Gustavsson, Thomas (2009). "Energy Flow in DNA Duplexes". Energy Transfer Dynamics in Biomaterial Systems. Springer Series in Chemical Physics. Vol. 93. pp. 127–142. doi:10.1007/978-3-642-02306-4_5. ISBN 978-3-642-02305-7.
  36. ^ Griesbeck, Axel; Oelgemöller, Michael; Ghetti, Francesco (2019). CRC Handbook of Organic Photochemistry and Photobiology, Third Edition - Two Volume Set. doi:10.1201/9780429100253. ISBN 978-0-429-10025-3.
  37. ^ https://link.springer.com/chapter/10.1007/128_2013_5111
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