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Related Concept Videos

Phosphodiester Linkages01:01

Phosphodiester Linkages

Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Other Nuclides: 31P, 19F, 15N NMR01:16

Other Nuclides: 31P, 19F, 15N NMR

Many organic, inorganic, and biological molecules contain spin-half nuclei such as nitrogen-15, fluorine-19, and phosphorus-31. As a result, NMR studies of these nuclei have found extensive applications in chemical and biological research.
While fluorine-19 and phosphorous-31 have high natural abundances (100%) and positive gyromagnetic ratios, nitrogen-15 has a low natural abundance and a negative gyromagnetic ratio. However, nitrogen-15 is still preferred over nitrogen-14 (which has a high...
Proton (¹H) NMR: Chemical Shift01:07

Proton (¹H) NMR: Chemical Shift

Organic molecules primarily contain carbon and hydrogen atoms. While all the hydrogen isotopes are NMR-active, protium or hydrogen-1 is the most abundant. It has a significant energy separation between its nuclear spin states due to its large gyromagnetic ratio. As per Boltzmann's distribution, an increase in the energy separation implies a greater excess population of nuclei available for excitation, resulting in a strong NMR absorption signal.
Absorption signals of all the protium nuclei in a...
NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
The DNA Helix01:16

The DNA Helix

Overview

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Related Experiment Video

Updated: Jun 18, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

DNA structures from phosphate chemical shifts.

Joséphine Abi-Ghanem1, Brahim Heddi, Nicolas Foloppe

  • 1INTS, INSERM S-665, Paris 75005, France.

Nucleic Acids Research
|November 28, 2009
PubMed
Summary

Nuclear magnetic resonance (NMR) reveals a direct link between phosphorus-31 chemical shifts and DNA structure. This finding enables a new method for refining DNA structures using NMR data alone.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for studying biomolecular structure and dynamics.
  • Phosphorus-31 (31P) chemical shifts in DNA are sensitive to the local electronic environment and can reflect structural parameters.
  • Understanding the relationship between NMR observables and DNA structural features is crucial for accurate structure determination.

Purpose of the Study:

  • To investigate the correlation between 31P chemical shifts and internucleotide distances in B-DNA.
  • To develop a novel method for DNA structure refinement using 31P chemical shift data.
  • To assess the utility of this method in capturing DNA properties in solution.

Main Methods:

  • Nuclear magnetic resonance (NMR) experiments were performed on B-DNA.

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Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins
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Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins

Published on: December 27, 2016

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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Last Updated: Jun 18, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins
12:47

Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins

Published on: December 27, 2016

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

  • Analysis of the linear correlation between 31P chemical shifts (deltaP) and three recurrent internucleotide distances.
  • Development of distance restraints directly derived from deltaP.
  • Integration of these restraints with molecular dynamics simulations in explicit solvent.
  • Testing the strategy on the Jun-Fos DNA oligomer.

    • Main Results:

    • A strong linear correlation was observed between deltaP and internucleotide distances in B-DNA.
    • This correlation demonstrates a tight coupling between phosphate group motions and DNA helicoidal parameters.
    • deltaP can be directly translated into distance restraints for structural refinement.
    • A novel method for refining DNA oligomers using exclusively deltaP-derived restraints was established.
    • Combined with molecular dynamics, this approach yielded detailed structural and dynamical insights comparable to conventional methods.

    Conclusions:

    • The study establishes a direct link between 31P chemical shifts and DNA structural parameters.
    • A new, straightforward method for DNA structure refinement using routine NMR data is presented.
    • This deltaP-based strategy offers a simple yet effective way to capture DNA solution properties, even from unlabeled samples.