Abstract

This amended new application seeks funding to characterize features of DNA electrostatics by observation of the free solution mobilities of a number of DNA molecules. The first goal is to measure the effect of net charge on the migration of DNA in an electric field. The second is to investigate the sequence dependence of the effective charge on the DNA molecule, following up on preliminary work indicating that this is the case. Combined with FRET analysis, the experiments proposed will challenge the hypothesis that monovalent counterion binding in the minor groove of DNA causes electrostatic collapse and leads to bending towards the minor groove. Further work entails an examination of the interaction between DNA and commonly used buffers in electrophoresis experiments.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM061009-02S1
Application #
6653714
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
2001-01-01
Project End
2004-12-31
Budget Start
2002-01-01
Budget End
2002-12-31
Support Year
2
Fiscal Year
2002
Total Cost
$83,460
Indirect Cost

  Institution

Name
University of Iowa
Department
Biochemistry
Type
Schools of Medicine
DUNS #
041294109
City
Iowa City
State
IA
Country
United States
Zip Code
52242

  Publications

Stellwagen, Nancy C (2017) Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory. J Phys Chem B 121:2015-2026
Stellwagen, Earle; Dong, Qian; Stellwagen, Nancy C (2015) Flanking A·T basepairs destabilize the B(?) conformation of DNA A-tracts. Biophys J 108:2291-9
Stellwagen, Earle; Stellwagen, Nancy C (2015) Electrostatic coupling between DNA and its counterions modulates the observed translational diffusion coefficients. Anal Chem 87:9042-6
Stellwagen, Nancy C; Lu, Yongjun (2010) Effect of magnesium ions and temperature on the sequence-dependent curvature of DNA restriction fragments. J Phys Condens Matter 22:494110
Stellwagen, Nancy C; Stellwagen, Earle (2009) Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 1216:1917-29
Stellwagen, Nancy C (2009) Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution. Electrophoresis 30 Suppl 1:S188-95
Dong, Qian; Stellwagen, Earle; Stellwagen, Nancy C (2009) Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 48:1047-55
Stellwagen, Earle; Prantner, Jason D; Stellwagen, Nancy C (2008) Do zwitterions contribute to the ionic strength of a solution? Anal Biochem 373:407-9
Stellwagen, Earle; Abdulla, Arian; Dong, Qian et al. (2007) Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Biochemistry 46:10931-41
Stellwagen, Earle; Stellwagen, Nancy C (2007) Quantitative analysis of cation binding to the adenosine nucleotides using the variable ionic strength method: validation of the Debye-Huckel-Onsager theory of electrophoresis in the absence of counterion binding. Electrophoresis 28:1053-62

Showing the most recent 10 out of 24 publications