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Related Concept Videos

Applications Of NMR In Biology01:25

Applications Of NMR In Biology

4.0K
Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
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Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

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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.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
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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.
1.2K
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...
942
Restriction Enzymes01:11

Restriction Enzymes

32.1K
Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
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Author Spotlight: Advancements in DNA Nanosensors &#8211; Addressing Sensitivity and Selectivity Challenges in Molecular Detection
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Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and Function.

Jan Borggräfe1,2, Manuel Etzkorn3,4,5

  • 1Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|February 28, 2022
PubMed
Summary
This summary is machine-generated.

This study explores DNAzymes, catalytic DNA molecules with unknown mechanisms. Solution Nuclear Magnetic Resonance (NMR) spectroscopy is presented as a powerful, cost-effective tool for structural and mechanistic DNAzyme characterization without isotope labeling.

Keywords:
DNAzymesHomonuclear NMRMetal-ion cofactorsNMR spectroscopyNucleic acids

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Catalytically active DNA oligomers, known as DNAzymes, possess diverse functions but their mechanisms remain poorly understood.
  • Lack of high-resolution structural insights hinders a complete understanding of DNAzyme mode-of-actions.
  • DNAzymes' characteristics, including size, flexibility, and cofactor interactions, make them suitable for NMR studies.

Purpose of the Study:

  • To provide protocols for the initial steps of NMR-based characterization of DNAzymes.
  • To enable mechanistic insights into DNAzyme function.
  • To facilitate DNAzyme research by focusing on cost-effective NMR experiments.

Main Methods:

  • Solution Nuclear Magnetic Resonance (NMR) spectroscopy is proposed as an optimal tool.
  • Focus on experiments that do not require expensive isotope labeling.
  • Detailed instructions and protocols for initial NMR characterization steps are provided.

Main Results:

  • NMR spectroscopy allows access to nearly all states of the DNAzyme and its substrate during the catalytic cycle.
  • The presented approaches reduce initial setup requirements for DNAzyme research.
  • Enables detailed mechanistic insights into DNAzyme catalytic activity.

Conclusions:

  • Solution NMR spectroscopy is a viable and accessible method for elucidating DNAzyme mechanisms.
  • The provided protocols can significantly lower the barrier to entry for DNAzyme structural and mechanistic studies.
  • This work aims to foster new research into the fundamental understanding and applications of DNAzymes.