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MPD and DNA bending in crystals and in solution
R E Dickerson1, D Goodsell, M L Kopka
1Department of Chemistry, University of California, Los Angeles 90095-1570, USA.
Journal of Molecular Biology
|February 16, 1996
Summary
DNA crystal structures reveal sequence-dependent bending, with A-tracts remaining straight. This bending, influenced by base stacking, supports a general-sequence bending model for DNA curvature.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- B-DNA duplexes exhibit sequence-dependent bending.
- MPD (2-methyl-2,4-pentanediol) concentration does not correlate with observed DNA bending.
- Two types of bends are identified: facultative hinges and a persistent bend in R-G-C-Y sequences.
Purpose of the Study:
- To investigate the sequence-dependence of DNA bending in B-DNA crystal structures.
- To explain the observed bending based on base stacking properties.
- To evaluate models of DNA macroscopic curvature using microscopic bending data.
Main Methods:
- Analysis of normal vector plots from B-DNA crystal structures.
- Examination of crystallographic data on DNA sequences, including A-tracts and non-A-tracts.
- MPD (2-methyl-2,4-pentanediol) gel retardation experiments.
Main Results:
- A-tracts are consistently straight, while other sequences exhibit bending (15-24 degrees).
- Facultative bends occur at junctions of G.C and A.T base pairs; a persistent bend is found in R-G-C-Y sequences.
- High MPD concentrations slightly reduce local bending but do not eliminate it.
- Crystallographic data supports a general-sequence bending model over others.
Conclusions:
- DNA bending is primarily sequence-dependent, with A-tracts being an exception.
- Base stacking properties, particularly of guanine and adenine, explain DNA bending.
- The general-sequence bending model is best supported by crystallographic evidence for DNA curvature.