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Address: 51 Newton Rd, 4-514 BSBIowa City, IA 52242Phone: (319) 335-7896
My laboratory studies sequence-dependent DNA structure using a variety of biophysical techniques, including gel and capillary electrophoresis, transient electric birefringence, fluorescence spectroscopy and circular dichroism. Current studies include:
DNA curvature. Although some DNA restriction fragments exhibit stable curvature of the helix backbone, the relationship between sequence and curvature is not well understood. We are currently investigating sequence-dependent DNA curvature by comparing naturally-occurring DNAs with derivatives missing one or more “bending elements”, and looking for previously unknown bending elements.
Preferential counterion binding. Previous studies have suggested that DNA curvature may be due to the preferential binding of counterions in the major and minor grooves of the DNA helix. We are investigating whether sequence dependent counterion binding actually occurs and how it varies with DNA sequence and the type of counterion.
Minihairpins.Certain DNA and RNA sequences form very stable minihairpins, with only 2 or 3 base pairs in the stem and 3 or 4 nucleotides in the loop. We are investigating the sequence dependence and thermal stability of a variety of minihairpins, in order to better understand the unusual stability of these structures.
Chang CY, Stellwagen NC. (2011) Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability. Biochemistry 50(42):9148-9157. PMID: 21942650
Stellwagen E, Muse JM, Stellwagen NC. (2011) Monovalent cation size and DNA conformational stability. Biochemistry 50(15):3084-3094. PMID: 21410141
Stellwagen, NC, Lu, YJ. (2010) Effect of magnesium ions and temperature on the sequence-dependent curvature of DNA restriction fragments. J Phys. Condens. Matter 22: 494110.
Stellwagen NC. Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution. Electrophoresis. 2009 Jun;30 Suppl 1:S188-95.
Dong Q, Stellwagen E, Stellwagen NC. Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry. 2009 Feb 10;48(5):1047-55.
Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A. 2009 Mar 6;1216(10):1917-29.
Lu Y, Stellwagen NC. Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts. Biophys J. 2008 Mar 1;94(5):1719-25.
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