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

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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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2D NMR: Overview of Homonuclear Correlation Techniques01:16

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Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
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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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Two-Dimensional (2D) NMR: Overview01:12

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The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
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Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
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2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)01:19

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Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...
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RNA Secondary Structure Determination by NMR.

Jonathan L Chen1,2, Stanislav Bellaousov2,3, Douglas H Turner4,5

  • 1Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627-0216, USA.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2016
PubMed
Summary

This study introduces NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS) software. It uses nuclear magnetic resonance (NMR) data to improve RNA secondary structure predictions, aiding 3D structure determination.

Keywords:
Chemical shiftsNAPSSNMRRNA secondary structure

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • RNA secondary structure prediction is crucial for understanding RNA function.
  • Existing methods often rely on thermodynamics and experimental restraints.
  • Nuclear magnetic resonance (NMR) provides valuable information on base pairing order and direction.

Purpose of the Study:

  • To describe a novel program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS).
  • To constrain RNA secondary structure predictions using NMR-derived base pairing information.
  • To facilitate the assignment of chemical shifts for 3D structure determination.

Main Methods:

  • Utilizes dynamic programming for RNA secondary structure prediction.
  • Incorporates experimental restraints from chemical mapping and 2D NMR spectra.
  • NAPSS-CS program uses base pair order (from NOESY) and chemical shifts as input.
  • Deduces 5'-3' direction of base pairs using chemical shifts.

Main Results:

  • NAPSS-CS successfully constrains secondary structure predictions based on NMR data.
  • Predicted structures facilitate chemical shift assignment to specific nucleotides.
  • The method is effective in revealing RNA pseudoknots.
  • Applicable to sequences with slowly exchanging structures.

Conclusions:

  • NAPSS-CS enhances RNA secondary structure prediction accuracy using NMR data.
  • The program aids in the crucial step of chemical shift assignment for 3D structure determination.
  • This approach is valuable for studying complex RNA structures like pseudoknots and alternative folds.