scholarly journals Evidence for a Solenoid Phase of Supercoiled DNA

2018 ◽  
Author(s):  
Andrew Dittmore ◽  
Keir C. Neuman
Keyword(s):  
Constant Force ◽  
Supercoiled Dna ◽  
Dna Molecule ◽  
Mechanical Manipulation ◽  
Measured Force ◽  
Single Dna Molecule

In mechanical manipulation experiments, a single DNA molecule overwound at constant force undergoes a discontinuous drop in extension as it buckles and forms a superhelical loop (a plectoneme). Further overwinding the DNA, we observe an unanticipated cascade of highly regular discontinuous extension changes associated with stepwise plectoneme lengthening. This phenomenon is consistent with a model in which the force-extended DNA forms barriers to plectoneme lengthening caused by topological writhe. Furthermore, accounting for writhe in a fluctuating solenoid gives an improved description of the measured force-dependent effective torsional modulus of DNA, providing a reliable formula to estimate DNA torque. Our data and model thus provide context for further measurements and theories that capture the structures and mechanics of supercoiled biopolymers.

The elastic theory of a single DNA molecule

Pramana ◽  
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

Label-free plasmonic assisted optical trapping of single DNA molecule

2021 ◽  
Author(s):  
Lei Chen ◽  
Wei Liu ◽  
Dongyi Shen ◽  
Zhihao Zhou ◽  
Yuehan Liu ◽  
...  
Keyword(s):  
Optical Trapping ◽  
Label Free ◽  
Dna Molecule ◽  
Single Dna Molecule

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

1994 ◽  
Vol 14 (2) ◽  
pp. 1520-1529
Author(s):  
C Liang ◽  
S A Gerbi
Keyword(s):  
Three Dimensional ◽  
Dna Amplification ◽  
Gel Method ◽  
Dna Molecule ◽  
Cutting Out ◽  
Origin Region ◽  
2D Gel ◽  
Third Dimension ◽  
Single Dna Molecule ◽  
Replication Intermediates

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.

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

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.

Thermophilic Topoisomerase I on a Single DNA Molecule

2003 ◽  
Vol 329 (2) ◽  
pp. 271-282 ◽  
Author(s):  
N.H Dekker ◽  
T Viard ◽  
C.Bouthier de La Tour ◽  
M Duguet ◽  
D Bensimon ◽  
...  
Keyword(s):  
Topoisomerase I ◽  
Dna Molecule ◽  
Single Dna Molecule

Micromanipulation of a Single DNA Molecule Using Laser Assembling of Microparticles

2001 ◽  
pp. 89-90
Author(s):  
Ken Hirano ◽  
Yukiko Matsuzawa ◽  
Yoshinobu Baba ◽  
Akira Mizuno
Keyword(s):  
Dna Molecule ◽  
Single Dna Molecule
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