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Related Concept Videos

2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

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...
2D NMR: Overview of Heteronuclear Correlation Techniques01:18

2D NMR: Overview of Heteronuclear Correlation Techniques

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis.
NMR Spectroscopy Of Amines01:19

NMR Spectroscopy Of Amines

In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is broad and...
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the others.
2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)01:19

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

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...
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

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 slanted or...

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Monitoring Protein-Ligand Interactions in Human Cells by Real-Time Quantitative In-Cell NMR using a High Cell Density Bioreactor
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Monitoring Protein-Ligand Interactions in Human Cells by Real-Time Quantitative In-Cell NMR using a High Cell Density Bioreactor

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RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Hakim Tafer1, Stephanie Kehr, Jana Hertel

  • 1Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria. htafer@tbi.univie.ac.at

Bioinformatics (Oxford, England)
|December 18, 2009
PubMed
Summary

RNAsnoop predicts H/ACA snoRNA targets for pseudouridine modifications. This tool identifies orphan snoRNAs responsible for modifications in human rRNAs and assigns targets for Drosophila H/ACA snoRNAs.

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NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
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Monitoring Protein-Ligand Interactions in Human Cells by Real-Time Quantitative In-Cell NMR using a High Cell Density Bioreactor
10:25

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Published on: March 9, 2021

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Small nucleolar RNAs (snoRNAs) guide chemical modifications of other RNAs.
  • The targets of many 'orphan' snoRNAs remain unidentified.
  • Box H/ACA snoRNAs mediate uridine to pseudouridine conversions via specific binding.

Purpose of the Study:

  • To develop an efficient and reliable tool for predicting H/ACA snoRNA target sites.
  • To identify the snoRNAs responsible for 'orphan' pseudouridine modifications in human rRNAs.
  • To assign targets for orphan H/ACA snoRNAs in Drosophila.

Main Methods:

  • Implementation of a dynamic programming algorithm for H/ACA-RNA interaction prediction.
  • Utilizing a support vector machine (SVM) for distinguishing true binding sites.
  • Incorporation of a system for evaluating comparative information.

Main Results:

  • RNAsnoop efficiently predicts thermodynamically optimal H/ACA-RNA interactions.
  • The tool successfully identified snoRNAs involved in human rRNA modifications.
  • A target was assigned to one of the five orphan H/ACA snoRNAs in Drosophila.

Conclusions:

  • RNAsnoop is an effective tool for predicting H/ACA snoRNA targets.
  • The study advanced the understanding of 'orphan' pseudouridine modifications.
  • The findings contribute to the functional annotation of non-coding RNAs.