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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

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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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¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

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A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
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NMR Spectroscopy: Spin–Spin Coupling01:08

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The spin state of an NMR-active nucleus can have a slight effect on its immediate electronic environment. This effect propagates through the intervening bonds and affects the electronic environments of NMR-active nuclei up to three bonds away; occasionally, even farther. This phenomenon is called spin–spin coupling or J-coupling. Coupling interactions are mutual and result in small changes in the absorption frequencies of both nuclei involved. While nuclei of the same element are involved...
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¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

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The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene...
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Spin–Spin Coupling: One-Bond Coupling01:17

Spin–Spin Coupling: One-Bond Coupling

1.2K
Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...
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Structural dynamics of a single-stranded RNA-helix junction using NMR.

Catherine D Eichhorn1, Hashim M Al-Hashimi2

  • 1Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA.

RNA (New York, N.Y.)
|April 19, 2014
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Summary

This study reveals how single-stranded RNA (ssRNA) tails near helix structures exhibit complex dynamics. This balance of order and disorder may aid in pseudoknot formation for ligand recognition.

Keywords:
RNA dynamicsligand recognitionprequeuosine riboswitchresidual dipolar couplingsspin relaxation

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Regulatory RNAs often feature single-stranded RNA (ssRNA) regions adjacent to structured elements.
  • Understanding the dynamics of these ssRNA tails is crucial for RNA function.

Purpose of the Study:

  • To investigate the dynamic properties of a 12-nucleotide ssRNA tail from a prequeuosine riboswitch.
  • To elucidate the structural and dynamic interplay at the ssRNA-helix junction.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy was employed.
  • Analysis included chemical shifts, NOE connectivity, (13)C spin relaxation, and residual dipolar coupling data.

Main Results:

  • The initial ssRNA residues (A25, U26) stack onto the adjacent helix, forming an ordered conformation.
  • The U26-A27 step acts as a pivot, initiating significant tail motions that increase towards the terminus.
  • Despite internal dynamics, the ssRNA tail maintains an average A-form helical conformation, coaxial with the helix.

Conclusions:

  • The ssRNA-helix junction displays intricate structural and dynamic complexity.
  • A balance between order and disorder in the ssRNA tail likely facilitates pseudoknot formation upon ligand binding.