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Base sequence effects on transport in DNA.

Esther M Conwell¹, Steven M Bloch

¹Department of Chemistry, University of Rochester, Rochester, New York 14627, USA. conwell@chem.rochester.edu

The Journal of Physical Chemistry. B

|March 17, 2006

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The polaron model accurately describes charge transport in DNA, explaining hole polarons in adenine sequences and extending to guanine sequences. Electron polarons are predicted to be similar in size to hole polarons.

Area of Science:

Biophysics
Computational Chemistry
Molecular Biology

Background:

The polaron model has successfully explained charge transport in DNA, particularly for hole polarons on adenine-rich sequences.
Understanding charge carrier behavior in DNA is crucial for various biological processes and potential applications.

Purpose of the Study:

To extend the polaron model to DNA sequences containing guanine (G) and other bases.
To investigate the formation and characteristics of polarons in diverse DNA sequences.
To compare the predicted polaron behavior with experimental data.

Main Methods:

Utilizing the polaron model based on solvation theory.
Performing calculations on DNA sequences such as AGGA and AGGGA.
Comparing theoretical predictions with experimental measurements of free energy differences and oxidative damage.

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Main Results:

Excellent agreement was found between the polaron model calculations and experimental free energy differences for guanine-containing sequences.
Experimental evidence supports hole polaron formation in DNA sequences with guanine and adenine.
The study suggests that charge transport in sequences with multiple thymines (T), AT, or GC pairs involves polarons with wave functions spanning both DNA strands.

Conclusions:

The polaron model provides a robust framework for understanding charge transport in various DNA sequences.
Both hole and electron polarons in DNA are predicted to be approximately 4-5 bases in size.
While polaron hopping is dominant in some repeated sequences, further research is needed for arbitrary sequences, especially concerning temperature-dependent properties.