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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair

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Monovalent cation localization in DNA A-tracts with different sequences.

Earle Stellwagen¹, Nancy C Stellwagen¹

¹Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA.

Electrophoresis

|June 24, 2023

Summary

DNA A-tracts exist in B and B* conformations in solution. Their fractional concentrations depend on lithium ion concentration, A-tract sequence, and overall A+T content, influencing DNA structure and behavior.

Keywords:

DNA A-tracts capillary electrophoresis internal ApT steps monovalent cation localization

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Area of Science:

Molecular Biology
Biophysics
Physical Chemistry

Background:

DNA A-tracts are specific DNA sequences known to influence DNA structure and function.
The conformation of DNA can be affected by the surrounding ionic environment.
Understanding DNA conformation is crucial for various biological processes and biotechnological applications.

Purpose of the Study:

To investigate the solution conformations of DNA oligomers containing A-tracts.
To determine how different sequences and ionic conditions affect A-tract conformation.
To elucidate the structural dynamics of A-tracts in response to cation concentration.

Main Methods:

Capillary electrophoresis was employed to measure the free solution mobilities of DNA oligomers.
Mobility measurements were performed using varying concentrations of lithium (Li+) and tetrapropylammonium (TPA+) ions in background electrolytes.
A 26-base pair (bp) random-sequence oligomer served as a reference for conformational analysis.

Main Results:

DNA A-tracts exhibit distinct conformations (B and B*) influenced by Li+ concentration.
The presence of an internal ApT step in A-tracts affects their conformational response to Li+ ions.
Oligomer A+T content modulates the conformational equilibrium between B and B* states.

Conclusions:

DNA A-tracts exist as a dynamic mixture of B and B* conformations in solution.
The conformational state is sensitive to Li+ ion concentration, A-tract sequence, and overall A+T content.
These findings provide insights into the sequence-dependent structural plasticity of DNA.