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Curved DNA molecules migrate anomalously slowly in free solution
Earle Stellwagen1, Yongjun Lu, Nancy C Stellwagen
1Department of Biochemistry, University of Iowa, Iowa City, IA, USA. nancy-stellwagen@uiowa.edu
Nucleic Acids Research
|August 9, 2005
Summary
Curved DNA fragments exhibit slower movement in gels and solution due to their structure. This anomalous mobility is linked to specific DNA sequences called A- and T-tracts, which independently influence the DNA bend.
Area of Science:
- Molecular Biology
- Biophysics
- Biochemistry
Background:
- DNA molecules can adopt curved structures.
- Electrophoretic mobility is a key property for analyzing DNA.
- The SV40 minichromosome contains DNA with specific structural features.
Purpose of the Study:
- To measure the electrophoretic mobility of a curved DNA restriction fragment.
- To investigate the relationship between DNA curvature and mobility.
- To identify the DNA sequence elements responsible for DNA bending and anomalous mobility.
Main Methods:
- Capillary electrophoresis was used to measure electrophoretic mobility in free solution and polyacrylamide gels.
- A 199 bp DNA restriction fragment from the SV40 minichromosome VP1 gene was analyzed.
- Sequence mutants of the DNA fragment were created and analyzed.
Main Results:
- The 199 bp DNA fragment exhibited an apparent bend angle of 46 degrees.
- The DNA fragment and its mutants with A-tracts migrated anomalously slowly in both free solution and gels.
- A- and T-tracts within the 'curvature module' were identified as the cause of curvature and anomalous mobility.
- Each A- or T-tract contributed independently but unequally to the DNA fragment's curvature.
Conclusions:
- Anomalously slow mobilities of curved DNA in gels are partly due to their slow mobilities in free solution.
- The spacing and presence of A- and T-tracts dictate their contribution to DNA curvature.
- Understanding DNA bending and mobility is crucial for molecular biology applications.