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Updated: Aug 3, 2026
09:06
Preparation of DNA-crosslinked Polyacrylamide Hydrogels
Published on: August 27, 2014
Relationship between curved DNA conformations and slow gel migration
R L Jernigan1, A Sarai, B Shapiro
1Laboratory of Mathematical Biology, National Cancer Institute, Bethesda, MD 20892.
Journal of Biomolecular Structure & Dynamics
|February 1, 1987
Summary
This study proposes specific DNA conformations to explain anomalous gel electrophoresis behavior. DNA sequences with alternating adenine/thymine bases form super-helical structures influencing their movement through gels.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- Previous work explored hydrophobic interactions in Adenine/Thymine (A/T) sequences.
- Aliphatic hydrocarbon groups in A/T sequences were previously analyzed for their role in DNA structure.
- Specific DNA sequences exhibit unusual behavior during gel electrophoresis.
Purpose of the Study:
- To propose specific DNA conformations that elucidate the anomalous gel electrophoretic behavior.
- To correlate molecular conformation with DNA migration patterns in gel electrophoresis.
- To explain the behavior of (VA4T4X)i and (V2A3T3X2)i sequences during electrophoresis.
Main Methods:
- Analysis of DNA molecular conformations, focusing on sequences with varying Adenine (A) and Thymine (T) bases.
- Modeling of super-helical structures formed by specific DNA sequences.
- Relating molecular conformation, specifically the moment of inertia, to experimental gel mobility data.
Main Results:
- Sequences like (VT4A4X)i may form tightly coiled super-helices, while (VA4T4X)i form broader super-helices.
- The sequence (V2A3T3X2)i forms a super-helix with a slightly smaller radius.
- A model correlating the ratio of apparent to actual molecular weight with the moment of inertia (I1) fits experimental gel mobility data.
- The ratio is found to be proportional to (I1)1/5.
Conclusions:
- Specific DNA conformations, particularly super-helical structures, directly influence gel electrophoretic behavior.
- The proposed model provides a molecular explanation for the observed anomalous migration of certain DNA sequences.
- The study highlights the importance of molecular conformation in interpreting DNA gel electrophoresis results.
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