Strong deformations of DNA: Effect on the persistence length
1Fakultät für Mathematik, Universität Wien, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria. kyrylo.simonov@univie.ac.at.
The European Physical Journal. E, Soft Matter
|September 28, 2018
Summary
This study reviews a method to calculate DNA persistence length, considering kinks. It enhances the Kratky-Porod model to measure how kinks reduce DNA flexibility.
Area of Science:
- Biophysics
- Molecular Biology
- Structural Biology
Background:
- DNA's physical properties are crucial for biological functions.
- Extreme DNA deformations, including kinks, significantly impact DNA mechanics.
- Understanding DNA flexibility is key to processes like replication and transcription.
Purpose of the Study:
- To review an approach for calculating DNA persistence length with kinks.
- To analyze how arbitrary kinks affect DNA's structural integrity.
- To provide a method for quantifying kink-induced changes in DNA flexibility.
Main Methods:
- Reviewing an enhanced Kratky-Porod model.
- Analyzing DNA double helix deformations.
- Measuring the reduction in persistence length due to kinks.
Main Results:
- The reviewed approach accurately calculates persistence length in kinked DNA.
- It quantifies the impact of kink configuration on DNA flexibility.
- The method identifies specific types and natures of DNA kinks.
Conclusions:
- The enhanced model provides a robust way to study kinked DNA.
- Understanding DNA kinks is vital for comprehending DNA mechanics in biological systems.
- This approach advances the study of DNA structural dynamics.
Keywords:
Living systems: Biological Matter
Related Concept Videos
02:28Titration Calculations: Strong Acid - Strong Base
34.0K
Calculating pH for Titration Solutions: Strong Acid/Strong Base
A titration is carried out for 25.00 mL of 0.100 M HCl (strong acid) with 0.100 M of a strong base NaOH. The pH at different volumes of added base solution can be calculated as follows:
(a) Titrant volume = 0 mL. The solution pH is due to the acid ionization of HCl. Because this is a strong acid, the ionization is complete and the hydronium ion molarity is 0.100 M. The pH of the solution is then:
A titration is carried out for 25.00 mL of 0.100 M HCl (strong acid) with 0.100 M of a strong base NaOH. The pH at different volumes of added base solution can be calculated as follows:
(a) Titrant volume = 0 mL. The solution pH is due to the acid ionization of HCl. Because this is a strong acid, the ionization is complete and the hydronium ion molarity is 0.100 M. The pH of the solution is then:
34.0K
03:22Strong Acid and Base Solutions
35.8K
A strong acid is a compound that dissociates completely in an aqueous solution and produces a concentration of hydronium ions equal to the initial concentration of acid. For example, 0.20 M hydrobromic acid will dissociate completely in water and produces 0.20 M of hydronium ions and 0.20 M of bromide ions.
35.8K
01:23Titration of a Strong Acid with a Strong Base
10.5K
During the titration of a strong acid with a strong base, pH calculations are primarily based on the concentration of residual hydronium or hydroxide ions. Initially, a strong acid like hydrochloric acid fully dissociates, creating hydronium and chloride ions, resulting in a low pH. The addition of a strong base like sodium hydroxide alters the concentration of hydronium ions by neutralizing them. As more base is added, the pH gradually increases. At the equivalence point, all hydronium ions...
10.5K
01:19Plastic Deformations
467
Plastic deformation represents a fundamental concept in materials science, which explains the irreversible change in the shape of a material when it experiences stress beyond its elastic capability. This phenomenon is important in structural engineering, especially in designing and analyzing cantilever beams—structures that are securely fixed at one end and bear loads at the opposite end. When these beams are subjected to loads within their elastic range, they will return to their...
467
01:14Plastic Deformations
453
It is essential to understand how structural members behave under plastic deformation when the bending stress exceeds the material's yield strength. This state of deformation permanently alters the shape of the member, in contrast to the linear elastic behavior observed before yielding. The strain at any point in the member is expressed in terms of maximum strain. Notably, the neutral axis, which coincides with the centroid during elastic bending, shifts away from the centroid under plastic...
453
01:12Temperature Dependent Deformation
407
In a nonhomogeneous rod made up of steel and brass, restrained at both ends and subjected to a temperature change, several steps are involved in calculating the stress and compressive load. Due to the problem's static indeterminacy, one end support is disconnected, allowing the rod to experience the temperature change freely. Next, an unknown force is applied at the free end, triggering deformations in the rod's steel and brass portions. These deformations are then calculated and added...
407