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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

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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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IR Frequency Region: Fingerprint Region01:03

IR Frequency Region: Fingerprint Region

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IR spectra are divided into two main regions: the diagnostic region and the fingerprint region. The diagnostic region of the spectrum lies above 1500 cm−1. The absorptions resulting from single-bond vibrations of the N–H, C–H, and O–H stretch at higher wavenumbers and appear on the left side of the spectrum. The stretching absorptions of the C≡C and C≡N occur between 2100–2300 cm−1. In contrast, those arising from stretching absorptions of the...
937
Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

722
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.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
722
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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UV–Vis Spectroscopy: Molecular Electronic Transitions01:16

UV–Vis Spectroscopy: Molecular Electronic Transitions

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In Ultraviolet–Visible (UV–Vis) spectroscopy, the absorption of electromagnetic radiation is used to probe the electronic structure of molecules. This technique provides insights into molecular electronic transitions, particularly the movement of electrons between different molecular orbitals. Radiation is absorbed if the energy of the electromagnetic radiation passing through the molecule is precisely equal to the energy difference between the excited and ground states. During this...
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¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

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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.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
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The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared

A Larasati Soenarjo1, Zhihao Lan2, Igor V Sazanovich3

  • 1Department of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom.

Journal of the American Chemical Society
|August 30, 2023
PubMed
Summary

G-quadruplexes (G4) are DNA structures crucial for gene regulation. This study used advanced spectroscopy and calculations to reveal the step-by-step folding process of G4-DNA, identifying key molecular interactions involved in its formation.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Chemical Physics

Background:

  • G-quadruplexes (G4) are DNA structures found in guanine-rich regions.
  • G4-DNA plays roles in gene transcription and telomere maintenance, making it a drug target.
  • Understanding G4-DNA's molecular interactions is key for rational drug design.

Purpose of the Study:

  • To investigate the molecular interactions driving G-quadruplex DNA folding.
  • To elucidate the folding sequence of a parallel-stranded G4-DNA using experimental and computational methods.

Main Methods:

  • Electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectroscopy was used to measure vibrational coupling spectra.
  • Quantum-chemical calculations using density functional theory (DFT) predicted coupling spectra for structural elements.
  • Structural changes during G4-DNA folding were monitored as a function of K+ ion concentration.

Main Results:

  • 102 vibrational coupling peaks were identified and tracked during the folding process.
  • Observed phenomena include frequency shifting, cross-peak intensity changes, and new peak appearances.
  • The study proposes a folding sequence for the Myc2345 G4-DNA under experimental conditions.

Conclusions:

  • Guanine quartets may pre-exist G4-DNA formation but remain unstacked.
  • Potassium ions (K+) are crucial for stacking these quartets and forming the complete G4 structure.
  • The combination of EVV 2DIR spectroscopy and DFT calculations provides insights into G4-DNA folding mechanisms.