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Department of Biochemistry

Research Interests

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.

Recent Publications

Stellwagen, E., Renze, A., and Stellwagen, N.C. (2007) Capillary electrophoresis is a sensitive monitor of the hairpin-random coil transition in DNA oligomers. Anal. Biochem. 365:103-110.

Stellwagen, E., Dong, Q., and Stellwagen, N.C. (2007) Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method. Biochemistry 46:2050-2058.

Stellwagen, E., and Stellwagen, N.C. (2007) Quantitative analysis of cation binding to the adenosine nucleotides using the variable ionic strength method: Validation of the Debye-Hückel-Onsager theory of electrophoresis in the absence of counterion binding. Electrophoresis 28:1053-1062.

Lu, Y., Stellwagen, E., and Stellwagen, N.C., (2006) Effect of organic cosolvents on the free solution mobility of curved and normal DNA molecules. Electrophoresis 27:1462-1470.

Stellwagen, N.C. (2006) Curved DNA molecules migrate anomalously slowly in polyacrylamide gels even at zero gel concentration. Electrophoresis 27:1163-1168.

Stellwagen, N.C. and Lu, Y.J. (2006) "Using Transient Electric Birefringence to Analyze Curvature in Naturally Occurring, Mixed-Sequence DNA Molecules," in Recent Advances in the Electro-Optics of Colloids, Polyelectrolytes and Biosystems, (Stoylov, S.P. and Stoimenova, M., Eds.) Marcel Dekker, New York, NY (in press).

Stellwagen, E., Lu, Y., Stellwagen, N. (2005) Curved DNA molecules migrate anomalously slowly in free solution. Nuc. Acid Res. 33:4425-4432. .

Stellwagen, E., Dong, Q., and Stellwagen, N.C. (2005) Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water. Biopolymers 72(2):62-68.

Stellwagen, N.C. and Mohanty, U. (Eds.) (2004) “Curvature and Deformation of Nucleic Acids: Recent Advances, New Paradigms,” Vol. 884 in ACS Symposium Series, American Chemical Society, Washington, D.C.

Lu, Y., Stellwagen, E., and Stellwagen, N.C. (2004) Inaccurate voltages reported by the Beckman/Coulter MDQ capillary electrophoresis system at low voltages lead to the calculation of erroneous electrophoresis mobilities. Anal. Biochem. 332:191-102.

Stellwagen, E. and Stellwagen, N.C. (2003) Probing the Electrostatic Shielding of DNA with Capillary Electrophoresis. Biophys. J. 84: 1855-1866.

Lu, Y., Weers, B.D. and Stellwagen, N.C. (2003) Mapping the Intrinsic DNA Bend in the M13 Origin of Replication by Atomic Force Microscopy. Biophys. J. 85: 409-415.

Lu, Y., Weers, B., and Stellwagen, N.C. (2003) Analysis of DNA Bending by Transient Electric Birefringence. Biopolymers 70: 270-288.

Dong, Q., Stellwagen, E., Dagle, J.M., Stellwagen, N.C. (2003) Free Solution Mobility of Small Single-Stranded Oligonucleotides with Variable Charge Densities. Electrophoresis 24: 3323-3329.

Stellwagen, N.C. (2003) Sequence-Dependent Bending in Plasmid pUC19. Electrophoresis 24: 3467-3475.

Stellwagen, E., Lu, Y.J., and Stellwagen, N.C. (2003) Unified Description of Electrophoresis and Diffusion in DNA and other Polyions. Biochemistry 42: 11745-11750.

Stellwagen, E., and Stellwagen, N.C. (2002) Determining the electrophoretic mobility and translational diffusion coefficients of DNA molecules in free solution. Electrophoresis 23: 2794-2803.

Lu, Y., Weers, B., and Stellwagen, N.C. (2002) DNA persistence length revisited. Biopolymers 61: 261-275.

Stellwagen, E., and Stellwagen, N.C. (2002) The free solution mobility of DNA in Tris-Acetate-EDTA buffers of different concentrations, with and without added NaC1. Electrophoresis 23: 1935-1941.

Allison, S.A., Li, Z., Reed, D., and Stellwagen, N.C. (2002) Modeling the Gel Electrophoresis of Short Duplex DNA by Brownian Dynamics: Cubic Gel Lattice with Direct Interaction. Electrophoresis 23: 2678-2689

Stellwagen, N.C. (2002) The Use of Transient Electric Birefringence to Characterize the Conformation of DNA in Solution, the Mechanism of DNA Gel Electrophoresis and the Structure of Agarose Gels. Colloids and Surfaces A 209: 107-122.

Stellwagen, N., Gelfi, C., Righetti, P.G. (2002) The Use of Gel and Capillary Electrophoresis to Investigate some of the Fundamental Physical Properties of DNA. Electrophoresis 23: 167-175.

Stellwagen, N.C., Bossi, A., Gelfi, C., Righetti, P. (2001) Do Orientation Effects Contribute to the Molecular Weight Dependence of the Free Solution Mobility of DNA? Electrophoresis 22: 4311-4315.

Stellwagen, N.C., Magnusdottir, S., Gelfi, C., and Righetti, P.G. (2001) Preferential Counterion Binding to A-Tract DNA Oligomers. J. Mol. Biol. 305: 1025-1033.

Stellwagen, N.C., Magnusdottir, S., Gelfi, C. and Righetti, P.G. (2001) Measuring the Translational Diffusion Coefficients of Small DNA Molecules by Capillary Electrophoresis. Biopolymers 58: 390-397.

Affiliations

Biochemistry Department

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