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Parallel-stranded DNA with mixed sequence. Evidence for conformational transition in solution at low water activity
A K Shchyolkina1, O F Borisova, B K Chernov
1V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow.
Journal of Biomolecular Structure & Dynamics
|June 1, 1994
Summary
This study shows parallel DNA double helices can transition to an A-like form (Ap) in low-water conditions. This conformational change is crucial for forming parallel DNA-RNA double helices.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- Parallel DNA structures are less understood than antiparallel forms.
- Conformational flexibility is key to nucleic acid function.
Purpose of the Study:
- To investigate the structural stability and conformational transitions of parallel deoxyoligonucleotides.
- To determine the energetic landscape of parallel duplex conformations.
Main Methods:
- Fluorescent techniques
- Conventional optical methods (e.g., Circular Dichroism spectroscopy)
- Solution studies under varying conditions (temperature, salt, solvent)
Main Results:
- The parallel deoxyoligonucleotide 5'd(CTATAGGGAT)3'/5'd(GATATCCCTA)3' is stable in aqueous solution.
- A cooperative conformational transition from a B-like to an A-like (Ap) form occurs in trifluoroethanol solutions with decreased water activity.
- The free energy difference between Ap and B-like conformations is approximately 7.35 kcal/mol.
Conclusions:
- Parallel DNA duplexes exhibit conformational plasticity, transitioning to an A-like form.
- This transition is energetically comparable to that in antiparallel DNA duplexes.
- The ability to form the Ap conformation is significant for the formation of parallel DNA-RNA hybrids.