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A structural transition in duplex DNA induced by ethylene glycol
Greg P Brewood1, Theresa Aliwarga, J Michael Schurr
1Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
The Journal of Physical Chemistry. B
|October 2, 2008
Summary
This study measured DNA supercoiling in ethylene glycol solutions, revealing a structural transition. The findings characterize two DNA states, providing insights into DNA mechanics and osmolytes.
Area of Science:
- Molecular Biophysics
- Biochemistry
- Structural Biology
Background:
- DNA supercoiling is governed by the twist energy parameter (ET).
- Ethylene glycol (EG) acts as an osmolyte, influencing DNA structure.
- Understanding DNA structural transitions is crucial for molecular biology.
Purpose of the Study:
- To measure the twist energy parameter (ET) and linking difference (Δl) of p30δ DNA in varying concentrations of ethylene glycol (EG).
- To develop a general theory for the effect of osmolytes on cooperative structural transitions in DNA.
- To characterize the properties of the two distinct DNA duplex states involved in the transition.
Main Methods:
- Experimental measurement of ET and Δl for p30δ DNA in solutions with 0-40% w/v EG.
- Analysis of ET versus water activity (aw) to identify structural transitions.
- Formulation of a general theory describing osmolyte effects on cooperative DNA transitions between two duplex states.
Main Results:
- A sigmoidal profile in ET vs. -ln aw indicated a discrete structural transition.
- Fitting the theoretical model to experimental data provided estimates for ET1, ET2, and transition midpoint parameters.
- The study inferred that at least 7-10% of base pairs exist in the transition state even in 0.1 M NaCl.
Conclusions:
- The transition involves a distinct second DNA state (state 2) with altered mechanical properties compared to state 1.
- State 2 exhibits a higher torsion elastic constant, lower bending elastic constant, and reduced twist energy.
- The transition is associated with changes in DNA-water/EG interactions, though the relative change in preferential interaction is slight.
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