Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method.

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

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Instrumentation For Quantitative Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100078584 ◽

1977 ◽

Vol 35 ◽

pp. 206-209

Author(s):

B. Ralph ◽

A.R. Jones

Keyword(s):

Volume Fraction ◽

Three Dimensional ◽

Two Dimensional ◽

Automatic Data ◽

Phase Volume Fraction ◽

Statistical Confidence ◽

Resultant Data ◽

Automatic Data Collection ◽

Third Dimension ◽

Evolution Of Microstructure

In all fields of microscopy there is an increasing interest in the quantification of microstructure. This interest may stem from a desire to establish quality control parameters or may have a more fundamental requirement involving the derivation of parameters which partially or completely define the three dimensional nature of the microstructure. This latter categorey of study may arise from an interest in the evolution of microstructure or from a desire to generate detailed property/microstructure relationships. In the more fundamental studies some convolution of two-dimensional data into the third dimension (stereological analysis) will be necessary.In some cases the two-dimensional data may be acquired relatively easily without recourse to automatic data collection and further, it may prove possible to perform the data reduction and analysis relatively easily. In such cases the only recourse to machines may well be in establishing the statistical confidence of the resultant data. Such relatively straightforward studies tend to result from acquiring data on the whole assemblage of features making up the microstructure. In this field data mode, when parameters such as phase volume fraction, mean size etc. are sought, the main case for resorting to automation is in order to perform repetitive analyses since each analysis is relatively easily performed.

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The elastic theory of a single DNA molecule

Pramana ◽

10.1007/bf02708315 ◽

2003 ◽

Vol 61 (2) ◽

pp. 353-360

Author(s):

Haijun Zhou ◽

Yang Zhang ◽

Zhang-Can Ou-Yang

Keyword(s):

Elastic Theory ◽

Dna Molecule ◽

Single Dna Molecule

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Theory of Electron Diffraction by Crystals

Zeitschrift für Naturforschung A ◽

10.1515/zna-1967-0402 ◽

1967 ◽

Vol 22 (4) ◽

pp. 422-431 ◽

Cited By ~ 111

Author(s):

Kyozaburo Kambe

Keyword(s):

Integral Equation ◽

Electron Diffraction ◽

General Theory ◽

Green’S Function ◽

Green's Function ◽

Scattering Problem ◽

Three Dimensional ◽

Two Dimensions ◽

The Third ◽

Third Dimension

A general theory of electron diffraction by crystals is developed. The crystals are assumed to be infinitely extended in two dimensions and finite in the third dimension. For the scattering problem by this structure two-dimensionally expanded forms of GREEN’S function and integral equation are at first derived, and combined in single three-dimensional forms. EWALD’S method is applied to sum up the series for GREEN’S function.

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Direct measurement of compression spring constant of single DNA molecule with AFM

Chinese Science Bulletin ◽

10.1360/982005-161 ◽

2005 ◽

Vol 50 (10) ◽

pp. 954 ◽

Cited By ~ 4

Author(s):

Xingfei ZHOU

Keyword(s):

Direct Measurement ◽

Spring Constant ◽

Dna Molecule ◽

Compression Spring ◽

Single Dna Molecule

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Label-free plasmonic assisted optical trapping of single DNA molecule

Optics Letters ◽

10.1364/ol.420957 ◽

2021 ◽

Author(s):

Lei Chen ◽

Wei Liu ◽

Dongyi Shen ◽

Zhihao Zhou ◽

Yuehan Liu ◽

...

Keyword(s):

Optical Trapping ◽

Label Free ◽

Dna Molecule ◽

Single Dna Molecule

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Modelling of form in thermotropic polymers

Philosophical Transactions of the Royal Society of London Series A Physical and Engineering Sciences ◽

10.1098/rsta.1994.0082 ◽

1994 ◽

Vol 348 (1686) ◽

pp. 73-96 ◽

Cited By ~ 5

Keyword(s):

Liquid Crystalline ◽

Main Chain ◽

Three Dimensional ◽

Point Singularity ◽

Dimensional Solution ◽

Crystalline Polymers ◽

Elasticity Equations ◽

Lower Total Energy ◽

Third Dimension ◽

Crystalline Microstructure

A lattice model of liquid crystalline microstructure has been developed. It provides the basis for the three-dimensional solution of the Frank elasticity equations for given boundary conditions while, in addition, providing a mechanistic representation of the development of texture as the microstructure relaxes with time. It is also able to represent disclination motion and the processes associated with their interaction. In particular, it has been used to study (s = ± 1/2) disclination loops, both those described by a single rotation vector, 17, and those in which 17 has a constant angular relationship with the loop line and are equivalent to a point singularity at a distance much larger than the loop radius. The application of the model to disclinations of unit strength, which are unstable both energetically and topologically, has shown that the decomposition into two 1/2 strength lines of lower total energy occurs much more readily than topological escape in the third dimension. The implication for structures observed in capillary tubes is discussed. The influence on microstructure of a splay constant much higher than that of twist or bend is explored in the context of main-chain liquid crystalline polymers, in particular, the stabilization of tangential +1 lines under such conditions is predicted in accord with observed microstructural features.

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Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.605102 ◽

2021 ◽

Vol 8 ◽

Author(s):

Youbin Mo ◽

Mounir Fizari ◽

Kristina Koharchik ◽

Douglas E. Smith

Keyword(s):

Optical Tweezers ◽

Dna Elasticity ◽

Dna Stretching ◽

Dna Molecule ◽

Scale Factors ◽

Length Measurements ◽

Microsphere Size ◽

Force Range ◽

Single Dna Molecule ◽

Displacement Measurements

We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25–45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.

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