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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
DNA Helicases00:55

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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
Mechanisms of Membrane-bending01:15

Mechanisms of Membrane-bending

The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
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Overview
DNA Topoisomerases02:02

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Updated: May 18, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations.

Ari Zeida1, Matías Rodrigo Machado, Pablo Daniel Dans

  • 1Institut Pasteur de Montevideo, Calle Mataojo 2020, Montevideo, Codigo Postal 11400, Uruguay.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 26, 2012
PubMed
Summary

DNA naturally bends due to thermal energy, forming kinks and internal bubbles. This intrinsic flexibility explains most DNA curvature observed in protein-bound structures, independent of protein interactions.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • DNA bending is crucial for biological processes.
  • Proteins stabilize DNA curvature, but intrinsic DNA flexibility is also suggested.
  • Understanding DNA's mechanical properties is essential.

Purpose of the Study:

  • To investigate the protein-independent flexibility of DNA.
  • To explore the role of thermal fluctuations in DNA kinking.
  • To quantify the contribution of thermally induced distortions to overall DNA curvature.

Main Methods:

  • Coarse-grained molecular dynamics simulations were employed.
  • Analysis of DNA curvature in simulated structures.
  • Comparison with experimentally determined DNA structures from the Protein Data Bank.

Main Results:

  • DNA exhibits thermally induced kinks due to spontaneous internal bubble formation.
  • These kinks significantly contribute to DNA's overall flexibility.
  • Simulated thermally induced distortions accounted for approximately 80% of DNA curvature in experimental structures.

Conclusions:

  • DNA possesses substantial intrinsic flexibility driven by thermal energy.
  • Thermally induced kinks are a major factor in DNA structural dynamics.
  • Protein-independent mechanisms play a dominant role in shaping DNA curvature.