SpringerLink
Log in

Fluorescence quenching of the SYBR Green I-dsDNA complex by in situ generated magnetic ionic liquids

  • Paper in Forefront
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

Abstract

Magnetic ionic liquids (MILs) with metal-containing cations are promising extraction solvents that provide fast and high efficiency extraction of DNA. Hydrophobic MILs can be generated in situ in a methodology called in situ dispersive liquid-liquid microextraction. To consolidate the sample preparation workflow, it is desirable to directly use the DNA-enriched MIL microdroplet in the subsequent analytical detection technique. Fluorescence-based techniques employed for DNA detection often utilize SYBR Green I, a DNA binding dye that exhibits optimal fluorescence when bound to double-stranded DNA. However, the MIL may hinder the fluorescence signal of the SYBR Green I-dsDNA complex due to quenching. In this study, MILs with metal-containing cations were selected and their fluorescence quenching effects evaluated using Fӧrster Resonance Energy Transfer and quantified using Stern-Volmer models. The MILs were based on N-substituted imidazole ligands (with butyl- and benzyl- groups as substituents) coordinated to Ni2+ or Co2+ metal centers as cations, and paired with chloride anions. The effects of NiCl2 and CoCl2 salts and of the 1-butyl-3-methylimidazolium chloride ionic liquid on the fluorophore complex were also studied to understand the components of the MIL structure that are responsible for quenching. The metal within the MIL chemical structure was found to be the main component contributing to fluorescence quenching. Fӧrster critical distances between 11.9 and 18.8 Å were obtained for the MILs, indicating that quenching is likely not due to non-radiative energy transfer but rather to spin-orbit coupling or excited-state electron transfer. The MILs were able to be directly used in qPCR and fluorescence emission measurements using a microplate reader for detection, demonstrating their applicability in fluorescence-based detection methods.

Graphical abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Yershov G, Barsky V, Belgovskiy A, Kirillov E, Kreindlin E, Ivanov I, et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A. 1996;93(10):4913–8. https://doi.org/10.1073/pnas.93.10.4913.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Evans WE, Relling MV. Moving towards individualized medicine with pharmacogenomics. Nature. 2004;429(6990):464–8. https://doi.org/10.1038/nature02626.

    Article  PubMed  CAS  Google Scholar 

  3. Butler JM. The future of forensic DNA analysis. Philos Trans R Soc B Biol Sci. 1674;2015(370). https://doi.org/10.1098/rstb.2014.0252.

  4. Newman ME, Parboosingh JS, Bridge PJ, Ceri H. Identification of archaeological animal bone by PCR/DNA analysis. J Archaeol Sci. 2002;29(1):77–84. https://doi.org/10.1006/jasc.2001.0688.

    Article  Google Scholar 

  5. Auricchio B, Anniballi F, Fiore A, Skiby JE, De Medici D. Evaluation of DNA extraction methods suitable for PCR-based detection and genoty** of Clostridium botulinum. Biosecur Bioterror. 2013;11(1):200–6. https://doi.org/10.1089/bsp.2012.0082.

    Article  Google Scholar 

  6. Nishi K, Isobe SI, Zhu Y, Kiyama R. Fluorescence-based bioassays for the detection and evaluation of food materials. Sensors. 2015;15(10):25831–67. https://doi.org/10.3390/s151025831.

    Article  PubMed  CAS  Google Scholar 

  7. Green MR, Sambrook J. Molecular cloning: a laboratroy manual. 4th ed. Cold Springs Harbor: Cold Springs Harbor Laboratory Press; 2012.

    Google Scholar 

  8. Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol. 2009;2009:1–10. https://doi.org/10.1155/2009/574398.

    Article  CAS  Google Scholar 

  9. Lienhard A, Schäffer S. Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ. 2019;7:1–17. https://doi.org/10.7717/peerj.6753.

    Article  CAS  Google Scholar 

  10. Gumińska N, Płecha M, Walkiewicz H, Hałakuc P, Zakryś B, Milanowski R. Culture purification and DNA extraction procedures suitable for next-generation sequencing of Euglenids. J Appl Phycol. 2018;30(6):3541–9. https://doi.org/10.1007/s10811-018-1496-0.

    Article  CAS  Google Scholar 

  11. Wang JH, Cheng DH, Chen XW, Du Z, Fang ZL. Direct extraction of double-stranded DNA into ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate and its quantification. Anal Chem. 2007;79(2):620–5. https://doi.org/10.1021/ac061145c.

    Article  PubMed  CAS  Google Scholar 

  12. Li T, Joshi MD, Ronning DR, Anderson JL. Ionic liquids as solvents for in situ dispersive liquid-liquid microextraction of DNA. J Chromatogr A. 2013;1272:8–14. https://doi.org/10.1016/j.chroma.2012.11.055.

    Article  PubMed  CAS  Google Scholar 

  13. Clark KD, Nacham O, Yu H, Li T, Yamsek MM, Ronning DR, et al. Extraction of DNA by magnetic ionic liquids: tunable solvents for rapid and selective DNA analysis. Anal Chem. 2015;87(3):1552–9. https://doi.org/10.1021/ac504260t.

    Article  PubMed  CAS  Google Scholar 

  14. Clark KD, Sorensen M, Nacham O, Anderson JL. Preservation of DNA in nuclease-rich samples using magnetic ionic liquids. RSC Adv. 2016;6(46):39846–51. https://doi.org/10.1039/c6ra05932e.

    Article  CAS  Google Scholar 

  15. Emaus MN, Clark KD, Hinners P, Anderson JL. Preconcentration of DNA using magnetic ionic liquids that are compatible with real-time PCR for rapid nucleic acid quantification. Anal Bioanal Chem. 2018:4135–44. https://doi.org/10.1007/s00216-018-1092-9.

  16. Clark KD, Varona M, Anderson JL. Ion-tagged oligonucleotides coupled with a magnetic liquid support for the sequence-specific capture of DNA. Angew Chem Int Ed Eng. 2017;56(26):7630–3. https://doi.org/10.1002/anie.201703299.

    Article  CAS  Google Scholar 

  17. Marengo A, Cagliero C, Sgorbini B, Anderson JL, Emaus MN, Bicchi C, et al. Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids. Plant Methods. 2019;15(1):1–11. https://doi.org/10.1186/s13007-019-0408-x.

    Article  Google Scholar 

  18. Clark KD, Emaus MN, Varona M, Bowers AN, Anderson JL. Ionic liquids: solvents and sorbents in sample preparation. J Sep Sci. 2018;41(1). https://doi.org/10.1002/jssc.201700864.

  19. Santos E, Albo J, Irabien A. Magnetic ionic liquids: synthesis, Properties and Applications. RSC Adv. 2014;4(75):40008–18. https://doi.org/10.1039/c4ra05156d.

    Article  CAS  Google Scholar 

  20. Clark KD, Nacham O, Purslow JA, Pierson SA, Anderson JL. Magnetic ionic liquids in analytical chemistry: a review. Anal Chim Acta. 2016;934:9–21. https://doi.org/10.1016/j.aca.2016.06.011.

    Article  PubMed  CAS  Google Scholar 

  21. Trujillo-Rodríguez MJ, Nan H, Varona M, Emaus MN, Souza ID, Anderson JL. Advances of ionic liquids in analytical chemistry. Anal Chem. 2019;91(1):505–31. https://doi.org/10.1021/acs.analchem.8b04710.

    Article  PubMed  CAS  Google Scholar 

  22. Sajid M. Magnetic ionic liquids in analytical sample preparation: a literature review. TrAC Trends Anal Chem. 2019;113:210–23. https://doi.org/10.1016/j.trac.2019.02.007.

    Article  CAS  Google Scholar 

  23. Hallett JP, Welton T. Room-temperature ionic liquids: solvents for synthesis and catalysis. 2. Chem Rev. 2011;111(5):3508–76. https://doi.org/10.1021/cr1003248.

    Article  PubMed  CAS  Google Scholar 

  24. Bowers AN, Trujillo-Rodríguez MJ, Farooq MQ, Anderson JL. Extraction of DNA with magnetic ionic liquids using in situ dispersive liquid – liquid microextraction. Anal Bioanal Chem. 2019;411:7375–85. https://doi.org/10.1007/s00216-019-02163-9.

    Article  PubMed  CAS  Google Scholar 

  25. Clark KD, Yamsek MM, Nacham O, Anderson JL. Magnetic ionic liquids as PCR-compatible solvents for DNA extraction from biological samples. Chem Commun. 2015;51(94):16771–3. https://doi.org/10.1039/c5cc07253k.

    Article  CAS  Google Scholar 

  26. Santra K, Clark KD, Maity N, Petrich JW, Anderson JL. Exploiting fluorescence spectroscopy to identify magnetic ionic liquids suitable for the isolation of oligonucleotides. J Phys Chem B. 2018;122:7747–56. https://doi.org/10.1021/acs.jpcb.8b05580.

    Article  PubMed  CAS  Google Scholar 

  27. Fleming GR. Chemical applications of ultrafast spectroscopy. New York: Oxford University Press; 1986.

    Google Scholar 

  28. Lakowicz JR. Principles of fluorescence spectroscopy. 3rd ed. New York: Springer; 2006.

    Book  Google Scholar 

  29. Stern O, Volmer M. Über die Abklingzeit der Fluoreszenz. Phys Z. 1919;20(183).

  30. Varnes AW, Dodson RB, Wehry EL. Interactions of transition-metal ions with photoexcited states of Flavins. Fluorescence quenching studies. J Am Chem Soc. 1972;94(3):946–50. https://doi.org/10.1021/ja00758a037.

    Article  PubMed  CAS  Google Scholar 

  31. Yue Q, Hou Y, Yue S, Du K, Shen T, Wang L, et al. Construction of an off-on fluorescence system based on carbon dots for trace pyrophosphate sensing. J Fluoresc. 2015;25(3):585–94. https://doi.org/10.1007/s10895-015-1538-9.

    Article  PubMed  CAS  Google Scholar 

  32. Yao C, Anderson JL. Dispersive liquid-liquid microextraction using an in situ metathesis reaction to form an ionic liquid extraction phase for the preconcentration of aromatic compounds from water. Anal Bioanal Chem. 2009;395(5):1491–502. https://doi.org/10.1007/s00216-009-3078-0.

    Article  PubMed  CAS  Google Scholar 

  33. Chand D, Farooq MQ, Pathak AK, Li J, Smith EA, Anderson JL. Magnetic ionic liquids based on transition-metal complexes with N-alkylimidazole ligands. New J Chem. 2019;43:20–3. https://doi.org/10.1039/C8NJ05176C.

    Article  CAS  Google Scholar 

  34. Fraiji LK, Hayes DM, Werner TC. Static and dynamic fluorescence quenching experiments for the physical chemistry laboratory. J Chem Educ. 1992;69(5):424. https://doi.org/10.1021/ed069p424.

    Article  CAS  Google Scholar 

  35. Lehrer SS. Solute Perturbation of protein fluorescence. The quenching of the tryptophyl fluorescence of model compounds and of lysozyme by iodide ion. Biochemistry. 1971;10(17):3254–63. https://doi.org/10.1021/bi00793a015.

    Article  PubMed  CAS  Google Scholar 

  36. Keizer J. Nonlinear fluorescence quenching and the origin of positive curvature in Stern-Volmer plots. J Am Chem Soc. 1983;105(6):1494–8. https://doi.org/10.1021/ja00344a013.

    Article  CAS  Google Scholar 

  37. Wang YQ, Zhang HM, Zhang GC, Tao WH, Tang SH. Interaction of the flavonoid hesperidin with bovine serum albumin: a fluorescence quenching study. J Lumin. 2007;126(1):211–8. https://doi.org/10.1016/j.jlumin.2006.06.013.

    Article  CAS  Google Scholar 

  38. **ng D, Dorr R, Cunningham RP, Scholes CP. Endonuclease III interactions with DNA substrates. 2. The DNA repair enzyme endonuclease III binds differently to intact DNA and to apyrimidinic/apurinic DNA substrates as shown by tryptophan fluorescence quenching. Biochemistry. 1995;34(8):2537–44. https://doi.org/10.1021/bi00008a018.

    Article  PubMed  CAS  Google Scholar 

  39. Förster T. Transfer mechanisms of electronic excitation energy. Radiat Res Suppl. 1960;2:326–39.

    Article  Google Scholar 

  40. Hunter CA, Sanders JKM. The nature of π-π interactions. J Am Chem Soc. 1990;112(14):5525–34. https://doi.org/10.1021/ja00170a016.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

J. L. A. acknowledges funding from the Chemical Measurement and Imaging Program at the National Science Foundation (CHE-1709372).

Author information

Authors and Affiliations

  1. Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA

    Ashley N. Bowers, Kalyan Santra, María J. Trujillo-Rodríguez, Anthony Song, Miranda N. Emaus, Jacob W. Petrich & Jared L. Anderson

Authors
  1. Ashley N. Bowers
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kalyan Santra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. María J. Trujillo-Rodríguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anthony Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Miranda N. Emaus
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jacob W. Petrich
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jared L. Anderson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jared L. Anderson.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals informed consent

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(PDF 1.11 mb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bowers, A.N., Santra, K., Trujillo-Rodríguez, M.J. et al. Fluorescence quenching of the SYBR Green I-dsDNA complex by in situ generated magnetic ionic liquids. Anal Bioanal Chem 412, 2743–2754 (2020). https://doi.org/10.1007/s00216-020-02538-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-020-02538-3

Keywords

Search

Navigation