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Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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NMR-Based Activity Assays for Determining Compound Inhibition, IC50 Values, Artifactual Activity, and Whole-Cell Activity of Nucleoside Ribohydrolases
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Quantifying functional group interactions that determine urea effects on nucleic acid helix formation.

Emily J Guinn1, Jeffrey J Schwinefus, Hyo Keun Cha

  • 1Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Journal of the American Chemical Society
|March 21, 2013
PubMed
Summary

Urea destabilizes nucleic acids and proteins. This study quantifies urea

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Area of Science:

  • Biophysical Chemistry
  • Molecular Biology
  • Chemical Thermodynamics

Background:

  • Urea is known to disrupt the structure of proteins, nucleic acids, and their complexes.
  • Understanding urea's interactions with biomolecules is crucial for probing conformational changes.
  • Previous studies characterized urea's interactions with protein functional groups.

Purpose of the Study:

  • To quantify the interactions between urea and nucleic acid components (bases, nucleosides, nucleotides).
  • To develop urea as a quantitative probe for conformational changes in nucleic acid processes.
  • To determine urea's interaction potentials with specific nucleic acid functional groups.

Main Methods:

  • Utilized osmometry and hexanol-water distribution assays to measure chemical potential derivatives (μ23).
  • Obtained interaction potentials by dissecting μ23 values for urea-nucleic acid component interactions.
  • Determined urea m-values for DNA dodecamer double helix formation.

Main Results:

  • Urea interacts favorably with nucleic acid functional groups (aromatic rings, carbonyl, phosphate, sugar) compared to water.
  • Interactions with heterocyclic aromatic rings and methyl groups are particularly favorable.
  • Urea m-values for DNA double helix formation (0.72-0.85 kcal mol(-1)m(-1)) showed little dependence on GC content.

Conclusions:

  • Extensive nucleobase stacking (60-90%) in separated DNA strands is necessary to explain observed urea m-values.
  • Results are consistent across DNA and RNA dodecamers at various temperatures and with literature data.
  • Urea serves as a valuable quantitative probe for changes in accessible surface area (ΔASA) during nucleic acid processes.