Plasmonic Manipulation of DNA using a Combination of Optical and Thermophoretic Forces: Separation of Different-Sized DNA from Mixture Solution.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
25 02 2020
25 02 2020
Historique:
received:
19
08
2019
accepted:
10
01
2020
entrez:
27
2
2020
pubmed:
27
2
2020
medline:
13
11
2020
Statut:
epublish
Résumé
We demonstrate the size-dependent separation and permanent immobilization of DNA on plasmonic substrates by means of plasmonic optical tweezers. We found that a gold nanopyramidal dimer array enhanced the optical force exerted on the DNA, leading to permanent immobilization of the DNA on the plasmonic substrate. The immobilization was realized by a combination of the plasmon-enhanced optical force and the thermophoretic force induced by a photothermal effect of the plasmons. In this study, we applied this phenomenon to the separation and fixation of size-different DNA. During plasmon excitation, DNA strands of different sizes became permanently immobilized on the plasmonic substrate forming micro-rings of DNA. The diameter of the ring was larger for longer DNA (in base pairs). When we used plasmonic optical tweezers to trap DNA of two different lengths dissolved in solution (φx DNA (5.4 kbp) and λ-DNA (48.5 kbp), or φx DNA and T4 DNA (166 kbp)), the DNA were immobilized, creating a double micro-ring pattern. The DNA were optically separated and immobilized in the double ring, with the shorter sized DNA and the larger one forming the smaller and larger rings, respectively. This phenomenon can be quantitatively explained as being due to a combination of the plasmon-enhanced optical force and the thermophoretic force. Our plasmonic optical tweezers open up a new avenue for the separation and immobilization of DNA, foreshadowing the emergence of optical separation and fixation of biomolecules such as proteins and other ncuelic acids.
Identifiants
pubmed: 32098985
doi: 10.1038/s41598-020-60165-5
pii: 10.1038/s41598-020-60165-5
pmc: PMC7042363
doi:
Substances chimiques
Gold
7440-57-5
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3349Références
Ashkin, A. Acceleration and Trapping of Particles by Radiation Pressure. Phys. Rev. Lett. 24, 156–159 (1970).
doi: 10.1103/PhysRevLett.24.156
Ashkin, A. & Dziedzic, J. M. Optical Levitation by Radiation Pressure. Appl. Phys. Lett. 19, 283–285 (1971).
doi: 10.1063/1.1653919
Ashkin, A., Dziedzic, J. M., Bjorkholm, J. E. & Chu, S. Observation of a single-beam gradient force optical trap for dielectric particles. Opt. Lett. 11, 288 (1986).
pubmed: 19730608
doi: 10.1364/OL.11.000288
Ashkin, A. Forces of a single-beam gradient laser trap on a dielectric sphere in the ray optics regime. Biophys. J. 61, 569–582 (1992).
pubmed: 19431818
pmcid: 1260270
doi: 10.1016/S0006-3495(92)81860-X
Chiu, D. T. & Zare, R. N. Biased Diffusion, Optical Trapping, and Manipulation of Single Molecules in Solution. J. Am. Chem. Soc. 118, 6512–6513 (1996).
doi: 10.1021/ja960978p
Yin, H. et al. Transcription Against an Applied Force. Science 270, 1653–1657 (1995).
pubmed: 7502073
doi: 10.1126/science.270.5242.1653
Smith, S. B., Cui, Y. & Bustamante, C. Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules. Science 271, 795–799 (1996).
pubmed: 8628994
doi: 10.1126/science.271.5250.795
Quake, S. R., Babcock, H. & Chu, S. The dynamics of partially extended single molecules of DNA. Nature 388, 151–154 (1997).
pubmed: 9217154
doi: 10.1038/40588
Bustamante, C., Bryant, Z. & Smith, S. B. Ten years of tension: single-molecule DNA mechanics. Nature 421, 423–427 (2003).
pubmed: 12540915
doi: 10.1038/nature01405
Grigorenko, A. N., Roberts, N. W., Dickinson, M. R. & Zhang, Y. Nanometric optical tweezers based on nanostructured substrates. Nat. Photonics 2, 365–370 (2008).
doi: 10.1038/nphoton.2008.78
Juan, M. L., Gordon, R., Pang, Y., Eftekhari, F. & Quidant, R. Self-induced back-action optical trapping of dielectric nanoparticles. Nat. Phys. 5, 915–919 (2009).
doi: 10.1038/nphys1422
Zhang, W., Huang, L., Santschi, C. & Martin, O. J. F. Trapping and Sensing 10 nm Metal Nanoparticles Using Plasmonic Dipole Antennas. Nano Lett. 10, 1006–1011 (2010).
pubmed: 20151698
doi: 10.1021/nl904168f
Tsuboi, Y. et al. Optical Trapping of Quantum Dots Based on Gap-Mode-Excitation of Localized Surface Plasmon. J. Phys. Chem. Lett. 1, 2327–2333 (2010).
doi: 10.1021/jz100659x
Quidant, R. Plasmonic tweezers—The strength of surface plasmons. MRS Bull. 37, 739–744 (2012).
doi: 10.1557/mrs.2012.172
Yan, H. et al. Biodegradable PLGA nanoparticles loaded with hydrophobic drugs: confocal Raman microspectroscopic characterization. J. Mater. Chem. B 3, 3677–3680 (2015).
doi: 10.1039/C5TB00434A
Hoshina, M., Yokoshi, N., Okamoto, H. & Ishihara, H. Super-Resolution Trapping: A Nanoparticle Manipulation Using Nonlinear Optical Response. ACS Photonics 5, 318–323 (2018).
doi: 10.1021/acsphotonics.7b01078
Zhao, Y., Saleh, A. A. E. & Dionne, J. A. Enantioselective Optical Trapping of Chiral Nanoparticles with Plasmonic Tweezers. ACS Photonics 3, 304–309 (2016).
doi: 10.1021/acsphotonics.5b00574
Lu, Y. et al. Tunable potential well for plasmonic trapping of metallic particles by bowtie nano-apertures. Sci. Rep. 6, 32675 (2016).
pubmed: 27666667
pmcid: 5036050
doi: 10.1038/srep32675
Tanaka, Y. & Sasaki, K. Optical trapping through the localized surface-plasmon resonance of engineered gold nanoblock pairs. Opt. Express 19, 17462 (2011).
pubmed: 21935112
doi: 10.1364/OE.19.017462
Cuche, A., Mahboub, O., Devaux, E., Genet, C. & Ebbesen, T. W. Plasmonic Coherent Drive of an Optical Trap. Phys. Rev. Lett. 108, 026801 (2012).
pubmed: 22324703
doi: 10.1103/PhysRevLett.108.026801
Shoji, T. et al. Reversible Photoinduced Formation and Manipulation of a Two-Dimensional Closely Packed Assembly of Polystyrene Nanospheres on a Metallic Nanostructure. J. Phys. Chem. C 117, 2500–2506 (2013).
doi: 10.1021/jp306405j
Tanaka, Y., Kaneda, S. & Sasaki, K. Nanostructured potential of optical trapping using a plasmonic nanoblock pair. Nano Lett. 13, 2146–50 (2013).
pubmed: 23547705
doi: 10.1021/nl4005892
Kotsifaki, D. G., Kandyla, M. & Lagoudakis, P. G. Plasmon enhanced optical tweezers with gold-coated black silicon. Sci. Rep. 6, 26275 (2016).
pubmed: 27195446
pmcid: 4872531
doi: 10.1038/srep26275
Ghorbanzadeh, M., Jones, S., Moravvej-Farshi, M. K. & Gordon, R. Improvement of Sensing and Trapping Efficiency of Double Nanohole Apertures via Enhancing the Wedge Plasmon Polariton Modes with Tapered Cusps. ACS Photonics 4, 1108–1113 (2017).
doi: 10.1021/acsphotonics.6b00923
Huft, P. R., Kolbow, J. D., Thweatt, J. T. & Lindquist, N. C. Holographic Plasmonic Nanotweezers for Dynamic Trapping and Manipulation. Nano Lett. 17, 7920–7925 (2017).
pubmed: 29144755
doi: 10.1021/acs.nanolett.7b04289
Jones, S., Andrén, D., Karpinski, P. & Käll, M. Photothermal Heating of Plasmonic Nanoantennas: Influence on Trapped Particle Dynamics and Colloid Distribution. ACS Photonics 5, 2878–2887 (2018).
doi: 10.1021/acsphotonics.8b00231
Yoo, D. et al. Low-Power Optical Trapping of Nanoparticles and Proteins with Resonant Coaxial Nanoaperture Using 10 nm Gap. Nano Lett. 18, 3637–3642 (2018).
pubmed: 29763566
doi: 10.1021/acs.nanolett.8b00732
Jensen, R. A. et al. Optical Trapping and Two-Photon Excitation of Colloidal Quantum Dots Using Bowtie Apertures. ACS Photonics 3, 423–427 (2016).
doi: 10.1021/acsphotonics.5b00575
Miyauchi, K., Tawa, K., Kudoh, S. N., Taguchi, T. & Hosokawa, C. Surface plasmon-enhanced optical trapping of quantum-dot-conjugated surface molecules on neurons cultured on a plasmonic chip. Jpn. J. Appl. Phys. 55, 06GN04 (2016).
doi: 10.7567/JJAP.55.06GN04
Mototsuji, A. et al. Plasmonic optical trapping of nanometer-sized J- /H- dye aggregates as explored by fluorescence microspectroscopy. Opt. Exp. 25, 13617 (2017).
doi: 10.1364/OE.25.013617
Pin, C. et al. Trapping and Deposition of Dye–Molecule Nanoparticles in the Nanogap of a Plasmonic Antenna. ACS Omega 3, 4878–4883 (2018).
pubmed: 31458703
pmcid: 6641714
doi: 10.1021/acsomega.8b00282
Toshimitsu, M. et al. Metallic-Nanostructure-Enhanced Optical Trapping of Flexible Polymer Chains in Aqueous Solution As Revealed by Confocal Fluorescence Microspectroscopy. J. Phys. Chem. C 116, 14610–14618 (2012).
doi: 10.1021/jp305247a
Shoji, T. et al. Highly Sensitive Detection of Organic Molecules on the Basis of a Poly(N -isopropylacrylamide) Microassembly Formed by Plasmonic Optical Trapping. Anal. Chem. 89, 532–537 (2017).
pubmed: 27959495
doi: 10.1021/acs.analchem.6b04024
Shoji, T. et al. Permanent Fixing or Reversible Trapping and Release of DNA Micropatterns on a Gold Nanostructure Using Continuous-Wave or Femtosecond-Pulsed Near-Infrared Laser Light. J. Am. Chem. Soc. 135, 6643–6648 (2013).
pubmed: 23586869
doi: 10.1021/ja401657j
Pang, Y. & Gordon, R. Optical Trapping of a Single Protein. Nano Lett. 12, 402–406 (2012).
pubmed: 22171921
doi: 10.1021/nl203719v
Tsai, W., Huang, J.-S. & Huang, C. Selective trapping or rotation of isotropic dielectric microparticles by optical near field in a plasmonic archimedes spiral. Nano Lett. 14, 547–52 (2014).
pubmed: 24392638
doi: 10.1021/nl403608a
Duhr, S., Arduini, S. & Braun, D. Thermophoresis of DNA determined by microfluidic fluorescence. Eur. Phys. J. E 15, 277–286 (2004).
pubmed: 15592768
doi: 10.1140/epje/i2004-10073-5
Duhr, S. & Braun, D. Why molecules move along a temperature gradient. Proc. Natl. Acad. Sci. 103, 19678–19682 (2006).
pubmed: 17164337
doi: 10.1073/pnas.0603873103
Jiang, H.-R. & Sano, M. Stretching single molecular DNA by temperature gradient. Appl. Phys. Lett. 91, 154104 (2007).
doi: 10.1063/1.2775810
Piazza, R. & Parola, A. Thermophoresis in colloidal suspensions. J. Phys. Condens. Matter 20, 153102 (2008).
doi: 10.1088/0953-8984/20/15/153102
Jiang, H.-R., Wada, H., Yoshinaga, N. & Sano, M. Manipulation of Colloids by a Nonequilibrium Depletion Force in a Temperature Gradient. Phys. Rev. Lett. 102, 208301 (2009).
pubmed: 19519079
doi: 10.1103/PhysRevLett.102.208301
Garcés-Chávez, V. et al. Extended organization of colloidal microparticles by surface plasmon polariton excitation. Phys. Rev. B 73, 085417 (2006).
doi: 10.1103/PhysRevB.73.085417
Wu, J. & Gan, X. Three dimensional nanoparticle trapping enhanced by surface plasmon resonance. Opt. Exp. 18, 27619–27626 (2010).
doi: 10.1364/OE.18.027619
Roxworthy, B. J. et al. Application of plasmonic bowtie nanoantenna arrays for optical trapping, stacking, and sorting. Nano Lett. 12, 796–801 (2012).
pubmed: 22208881
doi: 10.1021/nl203811q
Mel’nikov, S. M., Sergeyev, V. G. & Yoshikawa, K. Discrete Coil—Globule Transition of Large DNA Induced by Cationic Surfactant. J. Am. Chem. Soc. 117, 2401–2408 (1995).
doi: 10.1021/ja00114a004
Dias, R. S., Innerlohinger, J., Glatter, O., Miguel, M. G. & Lindman, B. Coil-globule transition of DNA molecules induced by cationic surfactants: A dynamic light scattering study. J. Phys. Chem. B 109, 10458–10463 (2005).
pubmed: 16852267
doi: 10.1021/jp0444464
Williams, M. C., Wenner, J. R., Rouzina, I. & Bloomfield, V. A. Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching. Biophys. J. 80, 1932–1939 (2001).
pubmed: 11259306
pmcid: 1301382
doi: 10.1016/S0006-3495(01)76163-2
Umazano, J. P. & Bertolotto, J. A. Optical properties of DNA in aqueous solution. J. Biol. Phys. 34, 163–177 (2008).
pubmed: 19669500
pmcid: 2577754
doi: 10.1007/s10867-008-9061-8
Braun, D. & Libchaber, A. Trapping of DNA by thermophoretic depletion and convection. Phys. Rev. Lett. 89, 188103 (2002).
pubmed: 12398641
doi: 10.1103/PhysRevLett.89.188103
Maeda, Y. T., Buguin, A. & Libchaber, A. Thermal Separation: Interplay between the Soret Effect and Entropic Force Gradient. Phys. Rev. Lett. 107, 038301 (2011).
pubmed: 21838407
doi: 10.1103/PhysRevLett.107.038301
Maeda, Y. T., Tlusty, T. & Libchaber, A. Effects of long DNA folding and small RNA stem-loop in thermophoresis. Proc. Natl. Acad. Sci. 109, 17972–17977 (2012).
pubmed: 23071341
doi: 10.1073/pnas.1215764109
Haynes, C. L., McFarland, A. D., Smith, M. T., Hulteen, J. C. & Van Duyne, R. P. Angle-resolved nanosphere lithography: Manipulation of nanoparticle size, shape, and interparticle spacing. J. Phys. Chem. B 106, 1898–1902 (2002).
doi: 10.1021/jp013570+
Takase, M. et al. Selection-rule breakdown in plasmon-induced electronic excitation of an isolated single-walled carbon nanotube. Nat. Photonics 7, 550–554 (2013).
doi: 10.1038/nphoton.2013.129
Shoji, T. & Tsuboi, Y. Plasmonic Optical Tweezers toward Molecular Manipulation: Tailoring Plasmonic Nanostructure, Light Source, and Resonant Trapping. J. Phys. Chem. Lett. 5, 2957–2967 (2014).
pubmed: 26278243
doi: 10.1021/jz501231h
Shoji, T. et al. Plasmon-Based Optical Trapping of Polymer Nano-Spheres as Explored by Confocal Fluorescence Microspectroscopy: A Possible Mechanism of a Resonant Excitation Effect. Jpn. J. Appl. Phys. 51, 092001 (2012).