Single-molecule studies of DNA mechanics

Department of Molecular and Cell Biology, Department of Physics, University of California, Berkeley, CA 94720, USA. carlos@alice.
Current Opinion in Structural Biology (Impact Factor: 7.2). 07/2000; 10(3):279-85. DOI: 10.1016/S0959-440X(00)00085-3
Source: PubMed


During the past decade, physical techniques such as optical tweezers and atomic force microscopy were used to study the mechanical properties of DNA at the single-molecule level. Knowledge of DNA's stretching and twisting properties now permits these single-molecule techniques to be used in the study of biological processes such as DNA replication and transcription.

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    • "Single-molecule force spectroscopy is a commonly used tool for the mechanical characterization of polymers and biological molecules, such as proteins and DNA [1] [2] [3] [4] [5] [6] [7] [8] [9] [10], and ligand-protein interactions [11] [12] [13] [14] [15] [16] [17] [18] [19]. These experiments can be performed using a variety of experimental setups, including optical tweezers [3] [20], the atomic force microscope (AFM) [1] [4], magnetic tweezers [21] [22], and the biomembrane force probe [23]. In a typical AFM single-molecule force spectroscopy experiment, protein molecules are immobilized on a surface, and the AFM probe is repeatedly brought into contact with the surface. "
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    ABSTRACT: Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)_{5} over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.
    Physical Review E 02/2015; 91(1-1):012710. · 2.29 Impact Factor
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    • "AFM probes can provide nanometer spatial resolution with a pN force resolution and has the ability to scan surfaces and measure the force curve of a target. However, the minimal force of 10 pN is too large, and it cannot provide 3D or long distance control [3]. A magnetic tweezer is a tool that can provide force from fN to mN. "
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    ABSTRACT: Photo-driven materials are an emerging research field due to its real-time definable capabilities and wide ranging potential applications. Previous research in the field has been limited to opto-electrical interactions. In this study, we investigated an opto-mechanical composite material of poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] and titanium oxide phthalocyanine (TiOPc). The characteristics of this developed composite material were examined using SEM, FTIR, and XRD analytical methods. Our results showed that a remnant polarization and coercive field can be increased with a proportional increase of TiOPc in the composite. Experimental results show that the optimal composition of the TiOPc to P(VDF-TrFE) was 10 wt% (d33 = 18 pC/N, 30% of impedance variation at 100 Hz). Our developed composite material has good potential as an opto-configurable mechanism for various applications.
    Materials Chemistry and Physics 01/2015; 149-150:254-260. DOI:10.1016/j.matchemphys.2014.10.014 · 2.26 Impact Factor
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    • "Some authors have speculated about the transport of coherent energy over distance to site-specific locations [41], although possible demonstrations of biochemical effect were not proposed. Treating the double-stranded DNA as a linear spring [46] with small displacements from equilibrium, we can obtain Hooke's constant k H = 3k B T /2P L, where P ≈ 50nm is the persistence length of DNA in physiological salt and L is the length of the strand. This corresponds to an oscillation frequency of approximately 3 × 10 9 radians per second and an energy six orders of magnitude smaller than that of ε P −O . "
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    ABSTRACT: Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize four-to-eight base pair sequences of palindromic DNA, cut both strands symmetrically, and act without an external metabolite such as ATP. While it is known that these enzymes induce strand breaks by attacking phosphodiester bonds, what remains unclear is the mechanism by which cutting occurs in concert at the catalytic centers. Previous studies indicate the primacy of intimate DNA contacts made by the specifically bound enzyme in coordinating the two synchronized cuts. We propose that collective electronic behavior in the DNA helix generates coherent oscillations, quantized through boundary conditions imposed by the endonuclease, that provide the energy required to break two phosphodiester bonds. Such quanta may be preserved in the presence of thermal noise and electromagnetic interference through decoherence shielding, the specific complex's exclusion of water and ions surrounding the helix. Clamping energy imparted by the enzyme decoherence shield is comparable with zero-point modes of the dipole-dipole oscillations in the DNA recognition sequence. The palindromic mirror symmetry of this sequence should conserve parity during the process. Experimental data corroborate that symmetric bond-breaking ceases when the symmetry of the endonuclease complex is violated, or when environmental parameters are perturbed far from biological optima. Persistent correlation between states in DNA sequence across spatial separations of any length--a characteristic signature of quantum entanglement--may be explained by such a physical mechanism.
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