Abstract

Here we report on the use of double-nanohole (DNH) optical tweezers as a label-free and free-solution single-molecule probe for protein–DNA interactions. Using this approach, we demonstrate the unzipping of individual 10 base pair DNA-hairpins, and quantify how tumor suppressor p53 protein delays the unzipping. From the Arrhenius behavior, we find the energy barrier to unzipping introduced by p53 to be 2 × 10−20 J, whereas cys135ser mutant p53 does not show suppression of unzipping, which gives clues to its functional inability to suppress tumor growth. This transformative approach to single molecule analysis allows for ultra-sensitive detection and quantification of protein–DNA interactions to revolutionize the fight against genetic diseases.

© 2014 Optical Society of America

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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
  30. R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
  32. M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
    [CrossRef] [PubMed]

2014

I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
[CrossRef] [PubMed]

A. Kotnala and R. Gordon, “Quantification of high-efficiency trapping of nanoparticles in a double nanohole optical tweezer,” Nano Lett.14(2), 853–856 (2014).
[CrossRef] [PubMed]

2013

A. Kotnala, D. DePaoli, and R. Gordon, “Sensing nanoparticles using a double nanohole optical trap,” Lab Chip13(20), 4142–4146 (2013).
[CrossRef] [PubMed]

P. N. Melentiev, A. E. Afanasiev, A. A. Kuzin, A. S. Baturin, and V. I. Balykin, “Giant optical nonlinearity of a single plasmonic nanostructure,” Opt. Express21(12), 13896–13905 (2013).
[CrossRef] [PubMed]

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE8(11), e80221 (2013).
[CrossRef] [PubMed]

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

2012

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Y. Pang and R. Gordon, “Optical trapping of a single protein,” Nano Lett.12(1), 402–406 (2012).
[CrossRef] [PubMed]

2011

M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics5(6), 349–356 (2011).
[CrossRef]

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper.56, 3405 (2011).

2010

K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
[CrossRef] [PubMed]

2009

L. Shokri, I. Rouzina, and M. C. Williams, “Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA,” Phys. Biol.6(2), 025002 (2009).
[CrossRef] [PubMed]

Y. F. Chen, G. A. Blab, and J. C. Meiners, “Stretching submicron biomolecules with constant-force axial optical tweezers,” Biophys. J.96(11), 4701–4708 (2009).
[CrossRef] [PubMed]

J. C. Waters, “Accuracy and precision in quantitative fluorescence microscopy,” J. Cell Biol.185(7), 1135–1148 (2009).
[CrossRef] [PubMed]

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

2008

D. B. Veprintsev and A. R. Fersht, “Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA,” Nucleic Acids Res.36(5), 1589–1598 (2008).
[CrossRef] [PubMed]

J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
[CrossRef] [PubMed]

K. C. Neuman and A. Nagy, “Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy,” Nat. Methods5(6), 491–505 (2008).
[CrossRef] [PubMed]

2007

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

2006

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

2004

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

2003

E. J. Peterman, F. Gittes, and C. F. Schmidt, “Laser-induced heating in optical traps,” Biophys. J.84(2), 1308–1316 (2003).
[CrossRef] [PubMed]

J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
[CrossRef] [PubMed]

2002

S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
[CrossRef] [PubMed]

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
[CrossRef] [PubMed]

2001

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

1999

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

1986

Abbondanzieri, E. A.

J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
[CrossRef] [PubMed]

Afanasiev, A. E.

Ashkin, A.

Bai, L.

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

Balhorn, R.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Balykin, V. I.

Baskin, R. J.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Baturin, A. S.

Bianco, P. R.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Bjorkholm, J. E.

Blab, G. A.

Y. F. Chen, G. A. Blab, and J. C. Meiners, “Stretching submicron biomolecules with constant-force axial optical tweezers,” Biophys. J.96(11), 4701–4708 (2009).
[CrossRef] [PubMed]

Block, S. M.

J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
[CrossRef] [PubMed]

Brandt, T.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Brewer, L. R.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Broekmans, O. D.

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Bustamante, C.

J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
[CrossRef] [PubMed]

Buzek, J.

J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
[CrossRef] [PubMed]

Carazo, J. M.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Chaurasiya, K. R.

K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
[CrossRef] [PubMed]

Chemla, Y. R.

J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
[CrossRef] [PubMed]

Chen, L.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Chen, Y.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Chen, Y. F.

Y. F. Chen, G. A. Blab, and J. C. Meiners, “Stretching submicron biomolecules with constant-force axial optical tweezers,” Biophys. J.96(11), 4701–4708 (2009).
[CrossRef] [PubMed]

Chen, Z.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Cherny, D.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

Cherny, D. I.

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

Chu, S.

Corzett, M.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Dantas Machado, A. C.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Dekker, L. C.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Delia, D.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

DePaoli, D.

A. Kotnala, D. DePaoli, and R. Gordon, “Sensing nanoparticles using a double nanohole optical trap,” Lab Chip13(20), 4142–4146 (2013).
[CrossRef] [PubMed]

Deppert, W.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

Dijk, M. A.

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

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[CrossRef] [PubMed]

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Eftekhari, F.

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

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G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

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I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

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M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

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M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
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R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
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M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
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R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
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E. J. Peterman, F. Gittes, and C. F. Schmidt, “Laser-induced heating in optical traps,” Biophys. J.84(2), 1308–1316 (2003).
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T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
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A. Kotnala and R. Gordon, “Quantification of high-efficiency trapping of nanoparticles in a double nanohole optical tweezer,” Nano Lett.14(2), 853–856 (2014).
[CrossRef] [PubMed]

A. Kotnala, D. DePaoli, and R. Gordon, “Sensing nanoparticles using a double nanohole optical trap,” Lab Chip13(20), 4142–4146 (2013).
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Y. Pang and R. Gordon, “Optical trapping of a single protein,” Nano Lett.12(1), 402–406 (2012).
[CrossRef] [PubMed]

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

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G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

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S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

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M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

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I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

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I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
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I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
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I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
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S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
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S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
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D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

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R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

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D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

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M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics5(6), 349–356 (2011).
[CrossRef]

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

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M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

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T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

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I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
[CrossRef] [PubMed]

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S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
[CrossRef] [PubMed]

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A. Kotnala and R. Gordon, “Quantification of high-efficiency trapping of nanoparticles in a double nanohole optical tweezer,” Nano Lett.14(2), 853–856 (2014).
[CrossRef] [PubMed]

A. Kotnala, D. DePaoli, and R. Gordon, “Sensing nanoparticles using a double nanohole optical trap,” Lab Chip13(20), 4142–4146 (2013).
[CrossRef] [PubMed]

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P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
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J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
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Laiho, M.

J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
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J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
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S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE8(11), e80221 (2013).
[CrossRef] [PubMed]

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R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
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J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
[CrossRef] [PubMed]

Laurens, N.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Lázaro, M.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

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S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

Lis, J. T.

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

Lukman, S.

S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE8(11), e80221 (2013).
[CrossRef] [PubMed]

Mameren, J.

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

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K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
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K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper.56, 3405 (2011).

Meiners, J. C.

Y. F. Chen, G. A. Blab, and J. C. Meiners, “Stretching submicron biomolecules with constant-force axial optical tweezers,” Biophys. J.96(11), 4701–4708 (2009).
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Melero, R.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Menges, C.

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Milstein, J. N.

K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper.56, 3405 (2011).

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J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
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K. C. Neuman and A. Nagy, “Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy,” Nat. Methods5(6), 491–505 (2008).
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S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
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K. C. Neuman and A. Nagy, “Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy,” Nat. Methods5(6), 491–505 (2008).
[CrossRef] [PubMed]

Palecek, E.

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

Paneni, M. S.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Pang, Y.

Y. Pang and R. Gordon, “Optical trapping of a single protein,” Nano Lett.12(1), 402–406 (2012).
[CrossRef] [PubMed]

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

Paramanathan, T.

K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
[CrossRef] [PubMed]

Pastore, E.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Peltonen, K.

J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
[CrossRef] [PubMed]

Perrone, F.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Peterman, E. J.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

E. J. Peterman, F. Gittes, and C. F. Schmidt, “Laser-induced heating in optical traps,” Biophys. J.84(2), 1308–1316 (2003).
[CrossRef] [PubMed]

Peterman, E. J. G.

I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
[CrossRef] [PubMed]

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Pierotti, M. A.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Pilotti, S.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Pricl, S.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Qin, P. Z.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Quidant, R.

M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics5(6), 349–356 (2011).
[CrossRef]

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

Raghunathan, K.

K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper.56, 3405 (2011).

Rajagopalan, S.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Reimann, M.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

Righini, M.

M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics5(6), 349–356 (2011).
[CrossRef]

Rohs, R.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Rouzina, I.

L. Shokri, I. Rouzina, and M. C. Williams, “Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA,” Phys. Biol.6(2), 025002 (2009).
[CrossRef] [PubMed]

Scheres, S. H.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Schmidt, C. F.

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

E. J. Peterman, F. Gittes, and C. F. Schmidt, “Laser-induced heating in optical traps,” Biophys. J.84(2), 1308–1316 (2003).
[CrossRef] [PubMed]

Schulten, K.

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

Shaevitz, J. W.

J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
[CrossRef] [PubMed]

Shokri, L.

L. Shokri, I. Rouzina, and M. C. Williams, “Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA,” Phys. Biol.6(2), 025002 (2009).
[CrossRef] [PubMed]

Shundrovsky, A.

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
[CrossRef] [PubMed]

Sitters, G.

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Smith, S. B.

J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
[CrossRef] [PubMed]

Striker, G.

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

Suardi, S.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Subramaniam, V.

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

Tamborini, E.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Valle, M.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

van den Wildenberg, S. M.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Veprintsev, D. B.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

D. B. Veprintsev and A. R. Fersht, “Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA,” Nucleic Acids Res.36(5), 1589–1598 (2008).
[CrossRef] [PubMed]

Verma, C. S.

S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE8(11), e80221 (2013).
[CrossRef] [PubMed]

Walter, K.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

Wang, M. D.

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
[CrossRef] [PubMed]

Warnecke, G.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

Waters, J. C.

J. C. Waters, “Accuracy and precision in quantitative fluorescence microscopy,” J. Cell Biol.185(7), 1135–1148 (2009).
[CrossRef] [PubMed]

Wende, W.

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Williams, M. C.

K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
[CrossRef] [PubMed]

L. Shokri, I. Rouzina, and M. C. Williams, “Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA,” Phys. Biol.6(2), 025002 (2009).
[CrossRef] [PubMed]

Wuite, G. J.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Wuite, G. J. L.

I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
[CrossRef] [PubMed]

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Yeh, Y.

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

Yu, J.

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

Zhang, X.

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Zhou, R.

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

Annu. Rev. Biochem.

J. R. Moffitt, Y. R. Chemla, S. B. Smith, and C. Bustamante, “Recent advances in optical tweezers,” Annu. Rev. Biochem.77(1), 205–228 (2008).
[CrossRef] [PubMed]

Biophys. J.

S. J. Koch, A. Shundrovsky, B. C. Jantzen, and M. D. Wang, “Probing protein-DNA interactions by unzipping a single DNA double helix,” Biophys. J.83(2), 1098–1105 (2002).
[CrossRef] [PubMed]

Y. F. Chen, G. A. Blab, and J. C. Meiners, “Stretching submicron biomolecules with constant-force axial optical tweezers,” Biophys. J.96(11), 4701–4708 (2009).
[CrossRef] [PubMed]

E. J. Peterman, F. Gittes, and C. F. Schmidt, “Laser-induced heating in optical traps,” Biophys. J.84(2), 1308–1316 (2003).
[CrossRef] [PubMed]

Chem. Rev.

I. Heller, T. P. Hoekstra, G. A. King, E. J. G. Peterman, and G. J. L. Wuite, “Optical tweezers analysis of DNA-protein complexes,” Chem. Rev.114(6), 3087–3119 (2014).
[CrossRef] [PubMed]

J. Biol. Chem.

T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem.277(43), 41192–41203 (2002).
[CrossRef] [PubMed]

J. Cell Biol.

J. C. Waters, “Accuracy and precision in quantitative fluorescence microscopy,” J. Cell Biol.185(7), 1135–1148 (2009).
[CrossRef] [PubMed]

J. Mol. Biol.

D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol.294(4), 1015–1026 (1999).
[CrossRef] [PubMed]

J. Phys. Chem. B

M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B108(20), 6479–6484 (2004).
[CrossRef] [PubMed]

J. Vis. Exper.

K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper.56, 3405 (2011).

Lab Chip

A. Kotnala, D. DePaoli, and R. Gordon, “Sensing nanoparticles using a double nanohole optical trap,” Lab Chip13(20), 4142–4146 (2013).
[CrossRef] [PubMed]

Mol. Cancer Ther.

M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther.5(6), 1467–1473 (2006).
[CrossRef] [PubMed]

Nano Lett.

Y. Pang and R. Gordon, “Optical trapping of a single protein,” Nano Lett.12(1), 402–406 (2012).
[CrossRef] [PubMed]

A. Kotnala and R. Gordon, “Quantification of high-efficiency trapping of nanoparticles in a double nanohole optical tweezer,” Nano Lett.14(2), 853–856 (2014).
[CrossRef] [PubMed]

Nat. Methods

K. C. Neuman and A. Nagy, “Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy,” Nat. Methods5(6), 491–505 (2008).
[CrossRef] [PubMed]

I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods10(9), 910–916 (2013).
[CrossRef] [PubMed]

Nat. Photonics

M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics5(6), 349–356 (2011).
[CrossRef]

Nat. Phys.

M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys.5(12), 915–919 (2009).
[CrossRef]

Nat. Struct. Mol. Biol.

M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol.16(2), 124–129 (2009).
[CrossRef] [PubMed]

Nat.Commun.

G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun.3, 1013 (2012).
[CrossRef] [PubMed]

Nature

P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature409(6818), 374–378 (2001).
[CrossRef] [PubMed]

J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature426(6967), 684–687 (2003).
[CrossRef] [PubMed]

Nucleic Acids Res.

D. B. Veprintsev and A. R. Fersht, “Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA,” Nucleic Acids Res.36(5), 1589–1598 (2008).
[CrossRef] [PubMed]

J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res.30(11), 2340–2348 (2002).
[CrossRef] [PubMed]

Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res.41(17), 8368–8376 (2013).
[CrossRef] [PubMed]

Opt. Express

Opt. Lett.

Phys. Biol.

L. Shokri, I. Rouzina, and M. C. Williams, “Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA,” Phys. Biol.6(2), 025002 (2009).
[CrossRef] [PubMed]

Phys. Life Rev.

K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev.7(3), 299–341 (2010).
[CrossRef] [PubMed]

PLoS ONE

S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE8(11), e80221 (2013).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. U.S.A.

R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A.108(2), 557–562 (2011).
[CrossRef] [PubMed]

Science

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science318(5848), 279–283 (2007).
[CrossRef] [PubMed]

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Figures (6)

Fig. 1
Fig. 1

Schematic of DNH laser tweezer trapping and unzipping DNA hairpins. The circular inset shows gold sample with DNH and DNA hairpins suspended in phosphate buffer solution. The rectangular inset is a scanning electron microscope (SEM) image of the DNH fabricated using focused ion beam (FIB). Abbreviation used: ODF = optical density filter; HWP = half wave plate; BE = beam expander; MR: mirror; OIMO: oil immersion microscope objective; APD = avalanche photodiode.

Fig. 2
Fig. 2

Trapping and unzipping 20 base DNA strands. a) Single strand DNA trapping event with no intermediate step b) A hairpin DNA trap event showing the unzipping with an intermediate step of ~0.1s. c) Energy reaction diagram of trapping and unzipping of DNA hairpin. k: Boltzmann constant, T: Temperature, U: Energy

Fig. 3
Fig. 3

Trapping and unzipping 12 bp DNA strand. The double strand 12bp DNA shows the unzipping with an intermediate step of ~0.01s.

Fig. 4
Fig. 4

Suppression of DNA hairpin unzipping by tumor suppressor protein p53. a) The wild type p53 suppresses the unzipping of the DNA hairpin for a delay of ~10 seconds. b) Comparison of cumulative probability of unzipping time ∆t for p53-DNA complex and DNA alone. c) Energy reaction diagram showing increased energy barrier ∆U equivalent to the binding energy ∆G of p53 and DNA.

Fig. 5
Fig. 5

Unzipping DNA hairpin and influence of mutant p53. a) The mutant p53 is incapable to suppress the unzipping of the DNA hairpin even though there is partial loss in binding activity (b) Cumulative probability of unzip time ∆t for mutant p53– DNA and hairpin DNA.

Fig. 6
Fig. 6

Weak optical trapping of p53 proteins. Optical trapping of p53 (a) wild-type and (b) mutant alone. Inset shows p53 protein structure.

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