Entropic elasticity of lambda-phage DNA
09 Sep 1994-Science (American Association for the Advancement of Science)-Vol. 265, Iss: 5178, pp 1599-1600
About: This article is published in Science.The article was published on 1994-09-09 and is currently open access. It has received 2089 citations till now.
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TL;DR: A review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena as mentioned in this paper.
Abstract: Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.
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Cites background from "Entropic elasticity of lambda-phage..."
...Nonlinear elastic effects follow from many polymer models; singlemolecule experiments indicate that the wormlike chain captures DNA elasticity particularly well Smith et al., 1992; Bustamante et al., 1994; Vologodskii, 1994; Marko and Siggia, 1995; Meiners and Quake, 2000 ....
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TL;DR: The atomic force microscope (AFM) is not only used to image the topography of solid surfaces at high resolution but also to measure force-versus-distance curves as discussed by the authors, which provide valuable information on local material properties such as elasticity, hardness, Hamaker constant, adhesion and surface charge densities.
3,281 citations
TL;DR: Single-molecule atomic force microscopy was used to investigate the mechanical properties of titin, the giant sarcomeric protein of striated muscle, and refolding of immunoglobulin domains was observed.
Abstract: Single-molecule atomic force microscopy (AFM) was used to investigate the mechanical properties of titin, the giant sarcomeric protein of striated muscle. Individual titin molecules were repeatedly stretched, and the applied force was recorded as a function of the elongation. At large extensions, the restoring force exhibited a sawtoothlike pattern, with a periodicity that varied between 25 and 28 nanometers. Measurements of recombinant titin immunoglobulin segments of two different lengths exhibited the same pattern and allowed attribution of the discontinuities to the unfolding of individual immunoglobulin domains. The forces required to unfold individual domains ranged from 150 to 300 piconewtons and depended on the pulling speed. Upon relaxation, refolding of immunoglobulin domains was observed.
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TL;DR: DsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B-form dsDNA, which may play a significant role in the energetics of DNA recombination.
Abstract: Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.
2,659 citations
TL;DR: The specific bonding of DNA base pairs provides the chemical foundation for genetics and this powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information.
Abstract: The specific bonding of DNA base pairs provides the chemical foundation for genetics. This powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the molecule.
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References
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TL;DR: Deviations from the force curves predicted by the freely jointed chain model suggest that DNA has significant local curvature in solution, and the effect of bend-inducing cis-diamminedichloroplatinum (II) was large and supports the hypothesis of natural curvatures in DNA.
Abstract: Single DNA molecules were chemically attached by one end to a glass surface and by their other end to a magnetic bead. Equilibrium positions of the beads were observed in an optical microscope while the beads were acted on by known magnetic and hydrodynamic forces. Extension versus force curves were obtained for individual DNA molecules at three different salt concentrations with forces between 10(-14) and 10(-11) newtons. Deviations from the force curves predicted by the freely jointed chain model suggest that DNA has significant local curvature in solution. Ethidium bromide and 4',6-diamidino-2-phenylindole had little effect on the elastic response of the molecules, but their extent of intercalation was directly measured. Conversely, the effect of bend-inducing cis-diamminedichloroplatinum (II) was large and supports the hypothesis of natural curvature in DNA.
1,826 citations
TL;DR: It is demonstrated that it is possible to determine the molar cyclization factor jM from single ligation reactions in which both circular and linear dimer DNA species are formed concurrently from linear monomers.
208 citations
TL;DR: In this article, a modified Gaussian probability for intrachain distances was used to account for polymer chain stiffness or excluded volume effects in non-Newtonian viscosity theory.
Abstract: Several attempts have been made to account for polymer chain stiffness or excluded volume effects in non‐Newtonian viscosity theory with the use of a modified Gaussian probability for intrachain distances. This method is here tested for the freely rotating chain by an application to the equilibrium expectation of the end‐to‐end vector R in the presence of an external potential −R· f. The Gaussian parameters are varied as f increases to keep Gaussian estimates of the bond length and bond angle constant. Numerical tests are made for the limits of a freely jointed chain and the worm chain, and the modified Gaussian approach is found to work very well.
190 citations