title: Mechanically unzipping dsDNA with built-in sequence inhomogeneities and bound proteins.
abstract: We theoretically analyze the force signal expected during unzipping through a single double-stranded DNA (dsDNA) molecule with designed subsequences or inhomogeneities with large stability differentials compared to the rest of the molecule. Our calculations describe experiments where the extension between the unzipped ends is fixed--the so-called fixed-extension ensemble--and the equilibrium force is measured. Two different types of force traces are obtained depending on the inhomogeneity length and strength. For short inhomogeneities, a "sawtooth" force trace is obtained, with a force jump corresponding to release of the entire inhomogeneity at once, as observed in unzipping of natural-sequence DNA (Bockelmann et al., Biophy. J. 82, 1537 (2002)). For longer inhomogeneities, traces with force plateaus are obtained, corresponding to a gradual unpeeling of the strongly bound region. We find that inhomogeneities are disrupted in sequence giving rise to a succession of force spikes superposed on the baseline unzipping force of 15pN. The height of the force pulses diminishes as regions further down the molecule are unzipped, and asymptotically the force response approaches that of DNA without large stability-enhanced islands. Our model also allows us to describe the transition between intact and disrupted binding zones by thermally activated kinetics. We then analyze the related situation where multiple proteins are bound at specific points on the DNA with or without cooperative interactions between proteins, and where the removal of each protein is required for unzipping to proceed further along the DNA. The proteins bind stably to dsDNA and also to single-stranded DNA (ssDNA) but with a lower binding enthalpy. The force jumps correspond to the extra mechanical work that has to be done to overcome the large protein binding enthalpy to either dsDNA or ssDNA. Each force jump leads to the dissociation of a corresponding protein, but we do not find simultaneous release of cooperatively stabilized proteins under the range of interactions strengths considered here. Our model is then used to describe recent experiments where the stability of nucleosome and nucleosome-analogues was assayed by mechanically unzipping the DNA template. Using physiological values of model parameters we find good agreement with the data.
authors: Department of Physics and Vitreous State Laboratory, The Catholic University of America, 620 Michigan Ave NE, 20064, Washington, DC, USA.
authors: Ping
authors: P
authors: Lu
authors: Ian L
authors: IL
authors: Pegg
authors: Abhijit
authors: A
authors: Sarkar
mesh_terms: D001483:Base Sequence; D001696:Biomechanical Phenomena; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D055595:Mechanical Phenomena; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D011506:Proteins
references: Curr Opin Struct Biol. 2000 Jun;10(3):303-10
references: 10851192
references: Nat Struct Mol Biol. 2006 Jun;13(6):549-54
references: 16732285
references: Biophys J. 2001 Sep;81(3):1324-32
references: 11509348
references: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8608-13
references: 11447279
references: Biophys J. 2002 Mar;82(3):1537-53
references: 11867467
references: Science. 2001 Apr 27;292(5517):733-7
references: 11326101
references: Biophys J. 2002 Aug;83(2):1098-105
references: 12124289
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan;75(1 Pt 1):011904
references: 17358181
references: Phys Rev Lett. 2002 Jun 17;88(24):248102
references: 12059334
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Sep;72(3 Pt 1):031906
references: 16241481
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3 Pt 1):031917
references: 11909119
references: Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11935-40
references: 9342340
references: Nature. 1999 Nov 4;402(6757):100-3
references: 10573426
references: Curr Opin Struct Biol. 2000 Jun;10(3):279-85
references: 10851197
references: Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12002-7
references: 11050232
references: Phys Rev Lett. 2000 Aug 14;85(7):1572-5
references: 10970557
references: Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746-50
references: 3459152
references: Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):127-32
references: 10618382
references: Genetica. 1999;106(1-2):57-62
references: 10710710
references: Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5
references: 9465037
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr;65(4 Pt 1):041907
references: 12005873