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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...
NMR and Mass Spectroscopy of Carboxylic Acids01:30

NMR and Mass Spectroscopy of Carboxylic Acids

In ¹H NMR spectroscopy, acidic protons (–COOH) of carboxylic acids are highly deshielded and absorb far downfield, at around 9–12 ppm. The chemical shift value depends on the concentration and solvent used.
While α protons of carboxylic acids absorb at 2–2.5 ppm, β protons absorb further upfield.
Carboxylic acids are easily identified by dissolving them in deuterium oxide, which results in a rapid exchange of the acidic protons with deuterium. This leads to the disappearance of the acidic...
Raman Spectroscopy: Overview01:20

Raman Spectroscopy: Overview

The underlying principle of Raman spectroscopy is based on the interaction between light and matter, specifically molecules' inelastic scattering of photons. When a monochromatic beam of light, typically from a laser source, interacts with a sample, most scattered light has the same frequency as the incident light. This is known as Rayleigh scattering.
However, a small fraction of the scattered light exhibits a frequency shift due to the exchange of energy between the incident photons and the...
NMR Spectroscopy of Aromatic Compounds01:14

NMR Spectroscopy of Aromatic Compounds

Aromatic compounds can be identified or analyzed using proton NMR and carbon‐13 NMR. Typically, aromatic hydrogens or hydrogens directly bonded to the aromatic rings are strongly deshielded by the aromatic ring current. Therefore, they absorb in the range of 6.5–8.0 ppm in proton NMR spectra. For instance, aromatic hydrogens directly bonded to the benzene ring absorb at 7.3 ppm. However, aromatic hydrogens of larger rings absorb farther upfield or downfield than the ideal range. Consider...
Molecular Structure and Acidity02:34

Molecular Structure and Acidity

An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
IR and UV–Vis Spectroscopy of Carboxylic Acids01:28

IR and UV–Vis Spectroscopy of Carboxylic Acids

In IR spectroscopy of carboxylic acids, the C=O bond shows a characteristic band between 1710 and 1760 cm⁻¹, and the O–H bond exhibits a broad band between 2500 and 3300 cm⁻¹.
However, the stretching absorptions for the C=O bond vary depending on the structure of carboxylic acids. The C=O bond of the free carboxylic acids shows a higher stretching frequency, 1760 cm−1, while H-bonded carboxylic acids (dimers) exhibit stretching absorptions at a lower frequency, 1710 cm−1. The C=O bond of the...

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Related Experiment Video

Updated: May 22, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
10:03

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

Published on: June 27, 2014

Nucleic Acid Structure Investigated by UV Resonance Raman Spectroscopy: Protonation Effects and A-Tract Structure.

L Sokolov1, K Wojtuszewski, E Tsukroff

  • 1a Molecular Biology and Biochemistry Department.

Journal of Biomolecular Structure & Dynamics
|May 22, 2012
PubMed
Summary

UV resonance Raman (UVRR) spectroscopy reveals pH-dependent tautomeric forms of purine bases. These spectral changes, including shifts in functional group modes, help identify protonated and enolate tautomers in DNA.

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Ultrafast Time-resolved Near-IR Stimulated Raman Measurements of Functional π-conjugate Systems
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Last Updated: May 22, 2026

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Ultrafast Time-resolved Near-IR Stimulated Raman Measurements of Functional π-conjugate Systems
09:57

Ultrafast Time-resolved Near-IR Stimulated Raman Measurements of Functional π-conjugate Systems

Published on: February 10, 2020

Area of Science:

  • Biophysical Chemistry
  • Spectroscopy
  • Molecular Biology

Background:

  • Purine bases (adenine, guanine, inosine) are fundamental to DNA and RNA.
  • Their chemical properties, including tautomerism, are pH-dependent.
  • Understanding these changes is crucial for molecular structure and function.

Purpose of the Study:

  • To investigate the pH-dependent tautomeric forms of purine bases using UV resonance Raman (UVRR) spectroscopy.
  • To identify specific spectral markers for protonated and enolate tautomers.
  • To explore the relevance of these findings in DNA structures.

Main Methods:

  • Utilized UV resonance Raman (UVRR) spectroscopy with excitation at 260 nm and 210 nm.
  • Analyzed the spectra of adenine, guanine, and inosine (as dAMP, dGMP, IMP) across a range of pH values.
  • Compared spectral features of DNA dodecamers with and without A-tracts.

Main Results:

  • Identified distinct UVRR spectral bands indicative of imino protonated tautomers at low pH (≤5.0) and enolate tautomers at high pH (≥10.0).
  • Observed characteristic shifts in the -NH(2) scissors mode for protonated dGMP and dAMP as pH decreased.
  • Found similar spectral features in A-tract DNA, attributing them to protonated dA residues and suggesting a link to 'bent' DNA.

Conclusions:

  • UVRR spectroscopy is effective in identifying pH-stabilized tautomeric forms of purine bases.
  • Specific spectral signatures can distinguish between different tautomeric states and protonation.
  • The observed spectral features in A-tract DNA suggest a potential spectroscopic marker for DNA conformation.