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Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels

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Abstract

Intercalating fluorescent probes are widely used to visualize DNA in studies on DNA-protein interactions. Some require the presence of adenosine triphosphate (ATP). We have investigated the mechanical properties of DNA stained with the fluorescent intercalating dyes YOYO-1 and YOYO-3 as a function of ATP concentrations (up to 2 mM) by stretching single molecules in nanofluidic channels with a channel cross-section as small as roughly 100 × 100 nm2. The presence of ATP reduces the length of the DNA by up to 11 %. On the other hand, negligible effects are found if DNA is visualized with the minor groove-binding probe 4′,6-diamidino-2-phenylindole. The apparent drop in extension under nanoconfinement is attributed to an interaction of the dye and ATP, and the resulting expulsion of YOYO-1 from the double helix.

Nanochannel-stretched DNA (48.5 kbp) stained with YOYO-1 is sensitive to ATP concentration in buffer. Nanochannels with a cross-section of 80 × 80 nm2 were used to stretch DNA.

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References

  1. Wirtz D (1995) Direct measurement of the transport properties of a single DNA molecule. Phys Rev Lett 75:2436–2439

    Article  CAS  Google Scholar 

  2. Bakajin O, Duke TAJ, Chou C et al (1998) Electrohydrodynamic stretching of DNA in confined environments. Phys Rev Lett 80:2737–2740. doi:10.1103/PhysRevLett.80.2737

    Article  CAS  Google Scholar 

  3. Perkins TT (1997) Single polymer dynamics in an elongational flow. Science 276:2016–2021. doi:10.1126/science.276.5321.2016

    Article  CAS  Google Scholar 

  4. Maier B, Rädler J (1999) Conformation and self-diffusion of single DNA molecules confined to two dimensions. Phys Rev Lett 82:1911–1914. doi:10.1103/PhysRevLett.82.1911

    Article  CAS  Google Scholar 

  5. Turner S, Cabodi M, Craighead H (2002) Confinement-induced entropic recoil of single DNA molecules in a nanofluidic structure. Phys Rev Lett 88:128103. doi:10.1103/PhysRevLett.88.128103

    Article  CAS  Google Scholar 

  6. Lam ET, Hastie A, Lin C et al (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30:771–776. doi:10.1038/nbt.2303

    Article  CAS  Google Scholar 

  7. Glazer A, Rye H (1992) Stable dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection. Nature 359:859–861

    Article  CAS  Google Scholar 

  8. Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA-molecules by using magnetic beads. Science 258:1122–1126

    Article  CAS  Google Scholar 

  9. Sischka A, Toensing K, Eckel R et al (2005) Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophys J 88:404–411. doi:10.1529/biophysj.103.036293

    Article  CAS  Google Scholar 

  10. Murade CU, Subramaniam V, Otto C, Bennink ML (2009) Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy. Biophys J 97:835–843. doi:10.1016/j.bpj.2009.05.024

    Article  CAS  Google Scholar 

  11. Reuter M, Dryden DTF (2010) The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA. Biochem Biophys Res Commun 403:225–229. doi:10.1016/j.bbrc.2010.11.015

    Article  CAS  Google Scholar 

  12. Doyle P, Ladoux B, Viovy J-L (2000) Dynamics of a tethered polymer in shear flow. Phys Rev Lett 84:4769–4772. doi:10.1103/PhysRevLett.84.4769

    Article  CAS  Google Scholar 

  13. Spielmann HP, Wemmer DE, Jacobsen JP (1995) Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy. Biochemistry 34:8542–8553

    Article  CAS  Google Scholar 

  14. Johansen F, Jacobsen JP (1998) 1H NMR studies of the bis-intercalation of a homodimeric oxazole yellow dye in DNA oligonucleotides. J Biomol Struct Dyn 16:205–222. doi:10.1080/07391102.1998.10508240

    Article  CAS  Google Scholar 

  15. Kundukad B, Yan J, Doyle PS (2014) Effect of YOYO-1 on the mechanical properties of DNA. Soft Matter 10:9721–9728. doi:10.1039/c4sm02025a

    Article  CAS  Google Scholar 

  16. Günther K, Mertig M, Seidel R (2010) Mechanical and structural properties of YOYO-1 complexed DNA. Nucleic Acids Res 38:6526–6532. doi:10.1093/nar/gkq434

    Article  Google Scholar 

  17. Kapuscinski J (1995) DAPI: a DNA-specific fluorescent probe. Biotech Histochem 70:220–233

    Article  CAS  Google Scholar 

  18. Meng X, Cai W, Schwartz DC (1996) Inhibition of restriction endonuclease activity by DNA binding fluorochromes. J Biomol Struct Dyn 13:945–951. doi:10.1080/07391102.1996.10508909

    Article  CAS  Google Scholar 

  19. Matsuzawa Y, Yoshikawa K (1994) Change of the higher order structure in a giant DNA induced by 4′, 6-diamidino-2-phenylindole as a minor groove binder and ethidium bromide as an intercalator. Nucleosides Nucleotides 13:1415–1423. doi:10.1080/15257779408012161

    Article  CAS  Google Scholar 

  20. Roushan M, Kaur P, Karpusenko A et al (2014) Probing transient protein-mediated DNA linkages using nanoconfinement. Biomicrofluidics 8:034113. doi:10.1063/1.4882775

    Article  Google Scholar 

  21. Tegenfeldt JO, Prinz C, Cao H et al (2004) The dynamics of genomic-length DNA molecules in 100-nm channels. Proc Natl Acad Sci U S A 101:10979–10983. doi:10.1073/pnas.0403849101

    Article  CAS  Google Scholar 

  22. Tree DR, Wang Y, Dorfman KD (2013) Extension of DNA in a nanochannel as a Rod-to-coil transition. Phys Rev Lett 110:208103. doi:10.1103/PhysRevLett.110.208103

    Article  Google Scholar 

  23. Reisner W, Beech J, Larsen N et al (2007) Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment. Phys Rev Lett 99:058302. doi:10.1103/PhysRevLett.99.058302

    Article  Google Scholar 

  24. Reisner W, Morton KJ, Riehn R et al (2005) Statics and dynamics of single DNA molecules confined in nanochannels. Phys Rev Lett 94:196101

    Article  Google Scholar 

  25. Karpusenko A, Carpenter JH, Zhou C et al (2012) Fluctuation modes of nanoconfined DNA. J Appl Phys 111:24701–247018. doi:10.1063/1.3675207

    Article  Google Scholar 

  26. Riehn R, Reisner W, Tegenfeldt JO et al (2007) Nanochannels for Genomic DNA Analysis: The Long and Short of It. In: Liu RH, Lee AP (eds) Integr. Biochips DNA Anal, 1st edn. Landes Bioscience, Austin, pp 151–186

    Chapter  Google Scholar 

  27. Riehn R, Lu MC, Wang YM et al (2005) Restriction mapping in nanofluidic devices. Proc Natl Acad Sci U S A 102:10012–10016. doi:10.1073/pnas.0503809102

    Article  CAS  Google Scholar 

  28. Carlsson C, Jonsson M, Akerman B (1995) Double bands in DNA gel electrophoresis caused by bis-intercalating dyes. Nucleic Acids Res 23:2413–2420

    Article  CAS  Google Scholar 

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Acknowledgments

We acknowledge support from the National Institutes of Health (R01GM107559), and thank Keith Weninger for fruitful discussions.

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Authors and Affiliations

  1. Department of Physics, NC State University, Raleigh, NC, 27695-8202, USA

    Maedeh Roushan, Zubair Azad, Shuang Fang Lim, Hong Wang & Robert Riehn

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  1. Maedeh Roushan
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  2. Zubair Azad
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  3. Shuang Fang Lim
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  4. Hong Wang
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  5. Robert Riehn
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Correspondence to Robert Riehn.

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Roushan, M., Azad, Z., Lim, S.F. et al. Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels. Microchim Acta 182, 1561–1565 (2015). https://doi.org/10.1007/s00604-015-1495-7

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  • DOI: https://doi.org/10.1007/s00604-015-1495-7

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