Unravelling DNA

Conroy, R. S.; Danilowicz, Claudia

doi:10.1080/00107510410001676786

Cited by 18 publications

(13 citation statements)

References 185 publications

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“…The electrostatic and van der Waals nonbonded potential energies between the first base of 16 adenine ssDNA and the nanotube membrane of 3.3 nm in length and 1.56 nm in diameter are plotted in Fig. 33 During the exit stage, a sufficiently strong electric field is necessary to assist the ssDNA to overcome the energy barrier in order to escape from the nanopore. The Coulomb interactions between the first base of the charged ssDNA molecule and CNT atoms appear to be negligible in comparison with the van der Waals interactions.…”

Section: Energetics Of Cnt-dna Interaction and The Effect Of Pore mentioning

confidence: 99%

Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane

Xie

Kong

Soh

et al. 2007

The Journal of Chemical Physics

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Molecular dynamics simulations based on a novel polarizable nanotube model were performed to study the dynamics in translocation of a single-stranded deoxyribonucleic acid oligonucleotide through a polarized carbon nanotube membrane by an applied electric field. The study revealed a nonlinear dependence of translocation velocity and an inverse quadratic dependence of translocation time on the electric field strength, as well as a threshold electric field below which the translocation process becomes impossible. The translocation rate was found to be pore-size dependent. The polarizable nanotube model developed for this study provides a useful platform for investigating the dynamics of a range of bionanosystems.

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Section: Energetics Of Cnt-dna Interaction and The Effect Of Pore mentioning

confidence: 99%

Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane

Xie

Kong

Soh

et al. 2007

The Journal of Chemical Physics

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“…In this sense, artificial force-induced separation of the double-stranded DNA is a tool to mimic and to understand such processes. Since a force probe can potentially accurately detect the binding strengths between complementary base pairs during the unzipping process, single-molecule mechanical unzipping of doublestranded DNA has been proposed as a possible sequencing method [15]. Several different experimental setups, such as optical tweezers [16] and atomic force microscopy [17], have been suggested for the mechanical unzipping of DNA in connection with possible fast and inexpensive sequencing.…”

Section: Forced Unzipping Of Dnamentioning

confidence: 99%

Nonlinearity in DNA and its Relation to Specific Functions

2009

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In memory of Alwyn Scott, we discuss the connection between the nonlinear dynamics of double-stranded DNA, experimental findings, and specific DNA functions. We begin by discussing how thermally induced localized openings (bubbles) of the DNA double-strand are important for interpreting dynamic force spectroscopy data. Then, we demonstrate a correlation between the sequence-dependent propensity for bubble formation and transcription initiation and other regulatory effects in viral DNA. Finally, we discuss the possibility of a connection between DNA dynamics and the ability of repair proteins to recognize ultraviolet-radiation damage.

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“…19 In addition, Evans 20 has developed a method using a deformable vesicle attached to a pipette to measure the forces between membrane-bound molecules and target specimen such as other vesicles or flat substrates. While providing important insights within their domains, these methods suffer from the invasiveness of the attached fiber, cantilever, or pipette, as well as the inherent limitations in the sensitivity of the measurement [typically 10 pN for atomic force microscopy (AFM), 1 pN for micropipette 21 ], and the number of directions that force may be applied.…”

Section: Introductionmentioning

confidence: 99%

“…[32][33][34][35][36][37] This method offers increased sensitivity over the mechanical probe methods discussed above, with sensitivity down to approximately 0.1 pN. 21 Its limitations are the achievable force (generally less than 200 pN), specimen heating at higher forces (approximately 10 °C/W of laser power at 1064 nm laser wavelength in water) 38,39 and the nonspecificity of forces which act on all refracting particles and macromolecules within the range of the optical trap. While laser heating is minimized with a trap using an 850 nm laser wavelength, 40 such lasers are not widely available at significant powers.…”

Section: Introductionmentioning

confidence: 99%

Thin-foil magnetic force system for high-numerical-aperture microscopy

Fisher

Cribb

Desai

et al. 2006

Review of Scientific Instruments

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Forces play a key role in a wide range of biological phenomena from single-protein conformational dynamics to transcription and cell division, to name a few. The majority of existing microbiological force application methods can be divided into two categories: those that can apply relatively high forces through the use of a physical connection to a probe and those that apply smaller forces with a detached probe. Existing magnetic manipulators utilizing high fields and high field gradients have been able to reduce this gap in maximum applicable force, but the size of such devices has limited their use in applications where high force and high-numerical-aperture (NA) microscopy must be combined. We have developed a magnetic manipulation system that is capable of applying forces in excess of 700 pN on a 1 μm paramagnetic particle and 13 nN on a 4.5 μm paramagnetic particle, forces over the full 4π sr, and a bandwidth in excess of 3 kHz while remaining compatible with a commercially available high-NA microscope objective. Our system design separates the pole tips from the flux coils so that the magnetic-field geometry at the sample is determined by removable thin-foil pole plates, allowing easy change from experiment to experiment. In addition, we have combined the magnetic manipulator with a feedback-enhanced, high-resolution (2.4 nm), highbandwidth (10 kHz), long-range (100 μm xyz range) laser tracking system. We demonstrate the usefulness of this system in a study of the role of forces in higher-order chromosome structure and function.

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Unravelling DNA

Cited by 18 publications

References 185 publications

Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane

Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane

Nonlinearity in DNA and its Relation to Specific Functions

Thin-foil magnetic force system for high-numerical-aperture microscopy

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