Abstract

RecA plays a central role in homologous recombination of DNA. When RecA combines with dsDNA to form RecA-dsDNA nucleofilament, it unwinds dsDNA and changes its structure. The unwinding length extension of a DNA segment interacting with RecA has been studied by various techniques, but the dynamic differential stiffness of dsDNA conjugating with RecA has not been well characterized. We applied oscillatory optical tweezers to measure the differential stiffness of dsDNA molecules, interacting with RecA, as a function of time at a constant stretching force of 33.6pN. The values of the differential stiffness of DNA (for stretching force in the range of 20.0pN to 33.6pN) measured by oscillatory optical tweezers, both before and after its interaction with RecA, are consistent with those measured by stationary optical tweezers. In the dynamic measurement, we have shown that the association (or binding) rate increases with higher concentration of RecA; besides, we have also monitored in real-time the dissociation of RecA from the stretched RecA-dsDNA filament as ATPγS was washed off from the sample chamber. Finally, we verified that RecA (I26C), a form of RecA mutant, does not affect the differential stiffness of the stretched DNA sample. It implies that mutant RecA (I26C) does not bind to the DNA, which is consistent with the result obtained by conventional biochemical approach.

© 2009 OSA

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  1. S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
    [CrossRef] [PubMed]
  2. C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
    [CrossRef] [PubMed]
  3. T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
    [CrossRef]
  4. S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
    [CrossRef] [PubMed]
  5. A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
    [CrossRef]
  6. T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
    [CrossRef] [PubMed]
  7. H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
    [CrossRef] [PubMed]
  8. F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
    [CrossRef] [PubMed]
  9. A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
    [CrossRef]
  10. B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
    [CrossRef]
  11. S. C. West, “Enzymes and molecular mechanisms of genetic recombination,” Annu. Rev. Biochem. 61(1), 603–640 (1992).
    [CrossRef] [PubMed]
  12. E. H. Egelman and A. Stasiak, “Electron microscopy of RecA-DNA complexes: two different states, their functional significance and relation to the solved crystal structure,” Micron 24(3), 309–324 (1993).
    [CrossRef]
  13. S. C. Kowalezykowski, “Biochemistry of genetic recombination: energetics and mechanism of DNA strand exchange,” Annu. Rev. Biophys. Biophys. Chem. 20(1), 539–575 (1991).
    [CrossRef]
  14. R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
    [CrossRef] [PubMed]
  15. M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
    [CrossRef] [PubMed]
  16. C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
    [CrossRef] [PubMed]
  17. M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
    [CrossRef]
  18. M.-T. Wei and A. Chiou, “Three-dimensional tracking of Brownian motion of a particle trapped in optical tweezers with a pair of orthogonal tracking beams and the determination of the associated optical force constants,” Opt. Express 13(15), 5798–5806 (2005), http://www.opticsinfobase.org/abstract.cfm?URI=oe-13-15-5798 .
    [CrossRef] [PubMed]
  19. L. A. Hough and H. D. Ou-Yang, “Viscoelasticity of aqueous telechelic poly (ethylene oxide) solutions: relaxation and structure,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73(3), 031802 (2006).
    [CrossRef] [PubMed]
  20. E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
    [CrossRef] [PubMed]
  21. M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
    [CrossRef] [PubMed]
  22. J. F. Marko and E. D. Siggia, “Stretching DNA,” Macromolecules 28(26), 8759–8770 (1995).
    [CrossRef]
  23. M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
    [CrossRef] [PubMed]

2008

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

2007

E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
[CrossRef] [PubMed]

2006

L. A. Hough and H. D. Ou-Yang, “Viscoelasticity of aqueous telechelic poly (ethylene oxide) solutions: relaxation and structure,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73(3), 031802 (2006).
[CrossRef] [PubMed]

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

2005

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

M.-T. Wei and A. Chiou, “Three-dimensional tracking of Brownian motion of a particle trapped in optical tweezers with a pair of orthogonal tracking beams and the determination of the associated optical force constants,” Opt. Express 13(15), 5798–5806 (2005), http://www.opticsinfobase.org/abstract.cfm?URI=oe-13-15-5798 .
[CrossRef] [PubMed]

2004

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

2003

B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
[CrossRef] [PubMed]

1999

M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
[CrossRef] [PubMed]

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

1997

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

1996

M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
[CrossRef]

S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
[CrossRef] [PubMed]

1995

J. F. Marko and E. D. Siggia, “Stretching DNA,” Macromolecules 28(26), 8759–8770 (1995).
[CrossRef]

1993

E. H. Egelman and A. Stasiak, “Electron microscopy of RecA-DNA complexes: two different states, their functional significance and relation to the solved crystal structure,” Micron 24(3), 309–324 (1993).
[CrossRef]

1992

S. C. West, “Enzymes and molecular mechanisms of genetic recombination,” Annu. Rev. Biochem. 61(1), 603–640 (1992).
[CrossRef] [PubMed]

1991

S. C. Kowalezykowski, “Biochemistry of genetic recombination: energetics and mechanism of DNA strand exchange,” Annu. Rev. Biophys. Biophys. Chem. 20(1), 539–575 (1991).
[CrossRef]

Albrecht, C.

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

Amitani, I.

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

Anselmetti, D.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Arias-Gonzalez, J. R.

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

Baskin, R. J.

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

Bennink, M. L.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Block, S. M.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Bryant, Z.

C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
[CrossRef] [PubMed]

Bustamante, C.

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
[CrossRef] [PubMed]

M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
[CrossRef] [PubMed]

S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
[CrossRef] [PubMed]

Chiou, A.

Chiu, C.-F.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Coleman, B. D.

B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
[CrossRef]

Cui, S.

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

Cui, Y.

S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
[CrossRef] [PubMed]

Dalal, R. V.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

de Grooth, B. G.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Dewalt, L. E.

M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
[CrossRef]

Eckel, R.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Egelman, E. H.

E. H. Egelman and A. Stasiak, “Electron microscopy of RecA-DNA complexes: two different states, their functional significance and relation to the solved crystal structure,” Micron 24(3), 309–324 (1993).
[CrossRef]

Galletto, R.

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

Gaub, H. E.

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

Gelles, J.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Greve, J.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Haruta, H.

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

Hegner, M.

M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
[CrossRef] [PubMed]

Homhuan, A.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Hough, L. A.

L. A. Hough and H. D. Ou-Yang, “Viscoelasticity of aqueous telechelic poly (ethylene oxide) solutions: relaxation and structure,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73(3), 031802 (2006).
[CrossRef] [PubMed]

Howard, J.

E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
[CrossRef] [PubMed]

Hu, S.-M.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Kanaar, R.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Kanger, J. S.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Kowalczykowski, S. C.

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

Kowalezykowski, S. C.

S. C. Kowalezykowski, “Biochemistry of genetic recombination: energetics and mechanism of DNA strand exchange,” Annu. Rev. Biophys. Biophys. Chem. 20(1), 539–575 (1991).
[CrossRef]

Kühner, F.

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

Landick, R.

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Lee, C.-D.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Leng, C.-H.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Li, H.-W.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

Liang, S.-M.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Mao, H.

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

Marko, J. F.

J. F. Marko and E. D. Siggia, “Stretching DNA,” Macromolecules 28(26), 8759–8770 (1995).
[CrossRef]

Mihardja, S.

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

Mizuno, R.

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

Morii, T.

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

Nørrelykke, S. F.

E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
[CrossRef] [PubMed]

Okada, T.

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

Olson, W. K.

B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
[CrossRef]

Ou-Yang, H. D.

L. A. Hough and H. D. Ou-Yang, “Viscoelasticity of aqueous telechelic poly (ethylene oxide) solutions: relaxation and structure,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73(3), 031802 (2006).
[CrossRef] [PubMed]

M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
[CrossRef]

Perkins, T. T.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

Ritort, F.

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

Ros, R.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Sakata-Sogawa, K.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Schäffer, E.

E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
[CrossRef] [PubMed]

Schärer, O. D.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Schins, J. M.

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

Sewald, N.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

Siggia, E. D.

J. F. Marko and E. D. Siggia, “Stretching DNA,” Macromolecules 28(26), 8759–8770 (1995).
[CrossRef]

Sischka, A.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Smith, S. B.

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
[CrossRef] [PubMed]

M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
[CrossRef] [PubMed]

S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
[CrossRef] [PubMed]

Stasiak, A.

E. H. Egelman and A. Stasiak, “Electron microscopy of RecA-DNA complexes: two different states, their functional significance and relation to the solved crystal structure,” Micron 24(3), 309–324 (1993).
[CrossRef]

Sun, H.-C.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Swigon, D.

B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
[CrossRef]

Tinoco, I.

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

Toensing, K.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Valentine, M. T.

M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
[CrossRef]

Wang, M. D.

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Wang, T.-F.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Wei, M.-T.

West, S. C.

S. C. West, “Enzymes and molecular mechanisms of genetic recombination,” Annu. Rev. Biochem. 61(1), 603–640 (1992).
[CrossRef] [PubMed]

Wilking, S. D.

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

Yin, H.

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Annu. Rev. Biochem.

S. C. West, “Enzymes and molecular mechanisms of genetic recombination,” Annu. Rev. Biochem. 61(1), 603–640 (1992).
[CrossRef] [PubMed]

Annu. Rev. Biophys. Biophys. Chem.

S. C. Kowalezykowski, “Biochemistry of genetic recombination: energetics and mechanism of DNA strand exchange,” Annu. Rev. Biophys. Biophys. Chem. 20(1), 539–575 (1991).
[CrossRef]

Biophys. J.

T. T. Perkins, H.-W. Li, R. V. Dalal, J. Gelles, and S. M. Block, “Forward and reverse motion of single RecBCD molecules on DNA,” Biophys. J. 86(3), 1640–1648 (2004).
[CrossRef] [PubMed]

H. Mao, J. R. Arias-Gonzalez, S. B. Smith, I. Tinoco, and C. Bustamante, “Temperature control methods in a laser tweezers system,” Biophys. J. 89(2), 1308–1316 (2005).
[CrossRef] [PubMed]

A. Sischka, K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti, “Molecular mechanisms and kinetics between DNA and DNA binding ligands,” Biophys. J. 88(1), 404–411 (2005).
[CrossRef]

M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, “Stretching DNA with optical tweezers,” Biophys. J. 72(3), 1335–1346 (1997).
[CrossRef] [PubMed]

Cytometry

M. L. Bennink, O. D. Schärer, R. Kanaar, K. Sakata-Sogawa, J. M. Schins, J. S. Kanger, B. G. de Grooth, and J. Greve, “Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1,” Cytometry 36(3), 200–208 (1999).
[CrossRef] [PubMed]

J. Am. Chem. Soc.

S. Cui, C. Albrecht, F. Kühner, and H. E. Gaub, “Weakly bound water molecules shorten single-stranded DNA,” J. Am. Chem. Soc. 128(20), 6636–6639 (2006).
[CrossRef] [PubMed]

J. Chem. Phys.

B. D. Coleman, W. K. Olson, and D. Swigon, “Theory of sequence-dependent DNA elasticity,” J. Chem. Phys. 118(15), 7127–7140 (2003).
[CrossRef]

J. Phys.: Condensed Matter (UK)

M. T. Valentine, L. E. Dewalt, and H. D. Ou-Yang, “Forces on a colloidal particle in polymer solution: a study using optical tweezers,” J. Phys.: Condensed Matter (UK) 8(47), 9477–9482 (1996).
[CrossRef]

Langmuir

E. Schäffer, S. F. Nørrelykke, and J. Howard, “Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers,” Langmuir 23(7), 3654–3665 (2007).
[CrossRef] [PubMed]

Macromolecules

J. F. Marko and E. D. Siggia, “Stretching DNA,” Macromolecules 28(26), 8759–8770 (1995).
[CrossRef]

Micron

E. H. Egelman and A. Stasiak, “Electron microscopy of RecA-DNA complexes: two different states, their functional significance and relation to the solved crystal structure,” Micron 24(3), 309–324 (1993).
[CrossRef]

Nature

R. Galletto, I. Amitani, R. J. Baskin, and S. C. Kowalczykowski, “Direct observation of individual RecA filaments assembling on single DNA molecules,” Nature 443(7113), 875–878 (2006).
[CrossRef] [PubMed]

C. Bustamante, Z. Bryant, and S. B. Smith, “Ten years of tension: single-molecule DNA mechanics,” Nature 421(6921), 423–427 (2003).
[CrossRef] [PubMed]

Opt. Express

Phys. Rev. E Stat. Nonlin. Soft Matter Phys.

L. A. Hough and H. D. Ou-Yang, “Viscoelasticity of aqueous telechelic poly (ethylene oxide) solutions: relaxation and structure,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73(3), 031802 (2006).
[CrossRef] [PubMed]

Phys. Rev. Lett.

F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, “Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers,” Phys. Rev. Lett. 96(11), 118301 (2006).
[CrossRef] [PubMed]

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

M. Hegner, S. B. Smith, and C. Bustamante, “Polymerization and mechanical properties of single RecA-DNA filaments,” Proc. Natl. Acad. Sci. U.S.A. 96(18), 10109–10114 (1999).
[CrossRef] [PubMed]

Protein Sci.

C.-D. Lee, H.-C. Sun, S.-M. Hu, C.-F. Chiu, A. Homhuan, S.-M. Liang, C.-H. Leng, and T.-F. Wang, “An improved SUMO fusion protein system for effective production of native proteins,” Protein Sci. 17(7), 1241–1248 (2008).
[CrossRef] [PubMed]

Rev. Sci. Instrum.

A. Sischka, R. Eckel, K. Toensing, R. Ros, and D. Anselmetti, “Compact microscope-based optical tweezers system for molecular manipulation,” Rev. Sci. Instrum. 74(11), 4827–4831 (2003).
[CrossRef]

Science

S. B. Smith, Y. Cui, and C. Bustamante, “Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules,” Science 271(5250), 795–799 (1996).
[CrossRef] [PubMed]

Thin Solid Films

T. Morii, R. Mizuno, H. Haruta, and T. Okada, “An AFM study of the elasticity of DNA molecules,” Thin Solid Films 464–465, 456–458 (2004).
[CrossRef]

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Figures (6)

Fig. 1
Fig. 1

A schematic diagram illustrating the attachment of DNA sample to two polystyrene particles, one at each end.

Fig. 2
Fig. 2

A schematic diagram of the experimental setup.

Fig. 3
Fig. 3

(a)~(c) A schematic illustration of the gradual stretching of a DNA sample by displacing one particle attached to one of its end while holding another particle attached to its other end via an optical tweezers.

Fig. 5
Fig. 5

(a)The steady-state force-extension relation of a naked dsDNA (left; denoted by “■”) and a RecA-conjugated dsDNA (right; denoted by “◆”) by the stationary optical tweezers approach. (b) The differential stiffness of a naked dsDNA segment (denoted by “■”) and a RecA-conjugated dsDNA segment (denoted by “◆”) as a function of optical stretching force measured by oscillatory optical tweezers with oscillation amplitude = 33nm, and oscillation frequency = 10Hz. In both cases the data were taken with the same DNA sample in the steady-state prior to and after its interaction with RecA.

Fig. 4
Fig. 4

Diagram of the forces on a trapped particle attached to a DNA sample under an oscillatory optical tweezers.

Fig. 6
Fig. 6

(a) The differential stiffness of the dsDNA sample stretched at a constant stretching force of 33.6pN as a function of time. From t = 100sec. to t = 1180sec., the measurement was taken as RecA was injected into the sample chamber to bind to the stretched dsDNA; from t = 1180sec. to t = 1750sec. the measurement was taken as de-ionized distilled water was injected into the sample chamber to dilute the concentration of ATPγS to dissociate RecA from the stretched DNA; (b) The differential stiffness (kDNA ) of the dsDNA sample stretched at a constant stretching force of 33.6pN as a function of time when RecA was injected with different concentration.

Equations (7)

Equations on this page are rendered with MathJax. Learn more.

mx¨(t)+6πηax˙(t)+kDNA[x(t)]=kOT[Aexp(iωt)-x(t)]
x=Dexp[i(ωtϕ)]
D=kOTA[(kDNA+kOT)]2+(6πηaω)2
ϕ=tan1[6πηaωkDNA+kOT]
kDNA=kOT(ADcosϕ1)
F=(kBTLA)(14(1-xL+FS)2-14+xL-FS)
FSxL1;  kDNAFxSL

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