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Related Experiment Videos

Preferential counterion binding to A-tract DNA oligomers.

N C Stellwagen1, S Magnusdottir, C Gelfi

  • 1Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA. nancy-stellwagen@uiowe.edu

Journal of Molecular Biology
|February 13, 2001
PubMed
Summary

DNA A-tracts, characterized by specific sequences, exhibit preferential binding of counterions. This binding influences DNA mobility, with certain A-tract sequences showing reduced electrophoretic mobility due to ion interactions.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • A-tracts are DNA sequences known for their unique structural properties, including bending.
  • The hypothesis suggests that the narrow minor groove of A-tracts facilitates site-specific monovalent counterion binding.
  • This binding is proposed to cause DNA bending through asymmetric charge neutralization and backbone collapse.

Purpose of the Study:

  • To investigate the hypothesis of preferential counterion binding in the minor groove of A-tract DNA.
  • To determine if counterion binding affects the solution mobility of DNA oligomers.
  • To correlate specific A-tract sequences with the degree of counterion binding.

Main Methods:

  • Measurement of free solution mobility of four 20 bp DNA oligomers using capillary electrophoresis.

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  • Comparison of DNA oligomers with and without A-tracts in Tris-acetate buffer.
  • Analysis of mobility changes with varying NaCl concentrations (1-20 mM).

    • Main Results:

    • DNA oligomers containing A-tracts exhibited reduced electrophoretic mobility compared to non-A-tract sequences.
    • The slowest mobility, indicating greatest counterion binding, was observed in a 20-mer with phased A3T3 runs.
    • Phased CACA sequences showed the fastest mobility, while A5 and T3A3 tracts displayed intermediate mobilities.
    • Similar mobility differences persisted with the addition of NaCl, supporting preferential binding.

    Conclusions:

    • The study provides evidence supporting preferential counterion binding within the minor groove of A-tract DNA.
    • The AnTn sequence motif appears particularly prone to this preferential counterion binding.
    • Counterion binding significantly influences the solution mobility of DNA oligomers, impacting their structural behavior.