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Related Concept Videos

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.
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...
The DNA Helix01:07

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
The DNA Helix01:16

The DNA Helix

Overview
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...

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Related Experiment Video

Updated: May 31, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Conformational flexibility of DNA.

Andriy Marko1, Vasyl Denysenkov, Dominik Margraf

  • 1Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany.

Journal of the American Chemical Society
|June 28, 2011
PubMed
Summary
This summary is machine-generated.

Pulsed Electron-Electron Double Resonance (PELDOR) reveals double-stranded DNA (ds-DNA) flexibility. Stretching ds-DNA induces a cooperative twist-stretch coupling, slightly reducing the helix radius.

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Last Updated: May 31, 2026

Studying DNA Looping by Single-Molecule FRET
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Area of Science:

  • Biophysics
  • Structural Biology
  • Molecular Dynamics

Background:

  • Conformational flexibility is crucial for DNA function.
  • Understanding DNA dynamics requires advanced spectroscopic techniques.
  • Existing models for DNA dynamics need experimental validation.

Purpose of the Study:

  • To investigate the conformational flexibility of helical DNA using PELDOR.
  • To determine stretching, twisting, and bending flexibility of ds-DNA.
  • To differentiate between various models of DNA dynamics.

Main Methods:

  • Utilized Pulsed Electron-Electron Double Resonance (PELDOR) spectroscopy.
  • Incorporated two rigid nitroxide spin labels into 20 base pair DNA duplexes.
  • Performed orientation-selective PELDOR experiments at X-band and G-band (2-4 nm distances).

Main Results:

  • Experimental data align with a dynamic model for ds-DNA.
  • Stretching of ds-DNA is coupled with a twist.
  • This cooperative twist-stretch coupling slightly reduces the helix radius.

Conclusions:

  • PELDOR is effective for probing DNA dynamics.
  • A cooperative twist-stretch coupling mechanism governs ds-DNA response to stretching.
  • The findings refine our understanding of DNA structural dynamics.