Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules

Science

Volumn 271, Issue 5250, 1996, Pages 795-799

  Smith, Steven B ^a   Cui, Yujia ^a   Bustamante, Carlos ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BUFFER; DNA B; DOUBLE STRANDED DNA; SINGLE STRANDED DNA; WATER;

ARTICLE; BACTERIOPHAGE LAMBDA; DNA CROSS LINKING; DNA RECOMBINATION; DNA STRUCTURE; ELASTICITY; ENERGY TRANSFER; FORCE; IONIC STRENGTH; NONHUMAN; PRIORITY JOURNAL; STRESS;

BASE COMPOSITION; CHEMISTRY, PHYSICAL; DNA; DNA, SINGLE-STRANDED; ELASTICITY; NUCLEIC ACID CONFORMATION; OSMOLAR CONCENTRATION; THERMODYNAMICS;

BACTERIOPHAGE LAMBDA;

EID: 0030024985     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.271.5250.795     Document Type: Article

References (36)

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6. ba) where / is the intensity of the light beam and c is the speed of light (S, Smith et al., in preparation). In accordance with this result, calibration of the force transducer has been shown by Stokes' law drag to be independent of the bead's size or of the buffer's refractive index.
7. BT (8). At 300 K, P would be 656 Å, or ∼ 193 bp.
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12. There are three ways to reconcile this discrepancy. The simplest way is to propose that dsDNA adopts a slightly altered conformation for F > 10 pN, and the Young's modulus value cannot be extrapolated to B-form DNA. A second approach would be to model dsDNA as a round deformable rod that is not made of a homogeneous material but rather from stiff material on the inside (where the bases stack) and compliant material on the outside (along the phosphates) A reduced "radius of stiffness" could then be defined consistent with the 150-bp persistence length. Such reduced radius would be ∼9 Å. A third explanation would retain the usually accepted radius for dsDNA (10 Å) and follow the suggestion of Trifonov and coworkers (11) that the stiffness of dsDNA, if it were inherently straight, would give it a persistence length of ∼200 bp but that the apparent persistence length is reduced to 150 bp by the presence of permanent bends along any random sequence of dsDNA If such numerous bends really exist, then the value of dsDNA stiffness obtained here is close to agreement with that estimated from less direct methods
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14. E N Trifonov, R. K. Z. Tan, S. C Harvey, in DNA Bending and Curvature, vol. 3 of Structure and Expression, W. K Olson, R H Sarma, M. Sundaralingam, Eds (Adenine, New York, 1987). pp 243-253. See also J. A. Schellman and S. C. Harvey, Biophys. Chem. 55, 95 (1995).
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19. Because a stretch-relax cycle takes ∼5 min, there is ample time for melting and reannealing to occur. Variability between molecules is due to the different placement and number of nicks
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21. B = ΔS/ΔL This expression is the Clapeyron-Claussius equator for a system subjected to mechanical deformation ΔS is then the discontinuous change in entropy accompanying the phase change and is proportional to the latent heat of the transition. Several processes may contribute to the entropy discontinuity, including the entropy change associated with the release of condensed ions and that associated with hydration changes in the molecule (see text)
22. B = ΔS/ΔL This expression is the Clapeyron-Claussius equator for a system subjected to mechanical deformation ΔS is then the discontinuous change in entropy accompanying the phase change and is proportional to the latent heat of the transition. Several processes may contribute to the entropy discontinuity, including the entropy change associated with the release of condensed ions and that associated with hydration changes in the molecule (see text)
23. B = ΔS/ΔL This expression is the Clapeyron-Claussius equator for a system subjected to mechanical deformation ΔS is then the discontinuous change in entropy accompanying the phase change and is proportional to the latent heat of the transition. Several processes may contribute to the entropy discontinuity, including the entropy change associated with the release of condensed ions and that associated with hydration changes in the molecule (see text)
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28. Betaine has been shown to lower the melting temperatures of CG base pairs to the same value as that of AT base pairs [W. A. Rees, T D. Yager, J. Korte, P H von Hippel, Biochemistry 32, 137 (1993)] Interestingly, the effect of betaine may have been just the opposite, that is, to enhance the difference between the forces required to induce the transition in AT- and CG-rich regions
29. The fitted Kuhn segment length of 15 Å implies a persistence length of 7.5 Å for ssDNA This value is about half that estimated by E K Achter and G Felsenfeld [Biopolymers 10, 1625 (1971)] for apurinated ssDNA by using light scattering and sedimentation It was assumed in that study that 1 M NaCI is a theta solvent for ssDNA. In the present study, the contractile force on a ssDNA molecule in 1 M NaCl, extrapolated to zero extension, was about 5 pN (see Fig 6, inset blue) This force offset probably indicates secondary structure formation or condensation within the molecule. If such structure formed in the sedimentation studies, then an erroneously large value for the rigidity of ssDNA and for RNA could have been obtained.
30. In the presence of adenosine triphosphate (ATP) or ATP[γ]S, RecA undergoes an alosteric change into a high-affinity form that binds dsDNA cooperatively in a stoichiometric ratio of 1 RecA/3 bp of dsDNA to form a right-handed helical filament [S C. West, Annu. Rev Biochem 61, 603 (1992)]. There are six RecA molecules and 18 6 bp/turn of the DNA molecule that is overstretched by a factor of 1.5 times its B-form contour length.
31. A Klug and F. H. C. Cnck [Nature 255, 530 (1975)] have suggested that formation of a few highly bent regions or "kinks" in DNA might be energetically favorable relative to smooth bending over a longer DNA length. The argument requires that after the ensuing of a localized kink in the DNA molecule, the energy required to bend the DNA further by an angle θ at that location, be smaller than the energy needed to bend the DNA by the same angle before the ensuing of the kink. This is indeed observed in macroscopic elastic media when the deformation goes beyond the elastic into the "plastic" regime (a plastic straw is a good example)
32. Carboxylate-polystyrene beads (3 54 μm in diameter, CV = 2.7%, Spherotech) were covalently coated with streptavidin using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC). Each molecule was pulled both right and left from the pipette to determine the point of attachment of the molecule on the pipette bead Because the optically trapped bead can rotate freely, but the pipette-trapped bead cannot, Ex can be determined in absolute units (micrometers). In each F-Ex curve, data representing the following four processes is superimposed: extending the molecule to right of the pipette, then relaxing it from the right, extending it leftward, then relaxing it from the left Each data point was taken after a ∼0 5 μm change in extension and a 2-s waiting period The force signal was then averaged for an additional 2 s and recorded. A complete right-left stretch cycle took about 10 min.
33. A video showing actual bead-DNA-bead assembly (Fig 1B) can be viewed on the World Wide Web at
34. D. W. Ussery, R W. Hoepfner, R. R. Sinden, Methods Enzymol 212, 242 (1992)
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36. We thank D. Stigter, E. Siggia, J. Marko, and A. Hausrath for many useful discussions. This work was supported by NSF grants MBC 90118482 and BIR 9318945, and by NIH grant GM-32543. Partial support was provided by the Lucille P. Markey Foundation