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DNA Electrophoresis in Agarose Gels

Title: DNA Electrophoresis in Agarose Gels: A New Mobility vs. DNA Length Dependence.
Name(s): Beheshti, Afshin, author
Van Winkle, David H., professor directing dissertation
Rill, Randolph L., outside committee member
Cao, Jianming, committee member
Bonesteel, Nicholas E., committee member
Riley, Mark A., committee member
Department of Physics, degree granting department
Florida State University, degree granting institution
Type of Resource: text
Genre: Text
Issuance: monographic
Date Issued: 2002
Publisher: Florida State University
Place of Publication: Tallahassee, Florida
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Separations were performed on double stranded DNA (dsDNA) using electrophoresis. Electrophoresis is the steady transport of particles under the influence of an external electric field. Double stranded DNA fragments ranging in length from 200 base pairs (bp) to 194,000 bp (0.34 nm = 1 bp) were electrophoresed at agarose gel concentrations T = 0:4%¡1:5%. The electric field was varied from 0.62 V/cm to 6.21 V/cm. A wide range of electric fields and gel concentrations were used to study the usefulness of a new interpolation equation, 1¹(L) =1¹L¡(1¹L¡1¹s)e¡L=°, where ¹L, ¹s, and ° are independent free fitting parameters. The long length mobility limit is interpreted as ¹L, the short length mobility limit is ¹s, and ° is the crossover between the long length limit and the short length limit. This exponential relation fit very well (Â2 ¸ 0:999) when there are two smooth transitions observed in the "reptation plots" (plotting 3¹L=¹± vs. L) (J. Rousseau, G. Drouin, and G. W. Slater, Phys Rev Lett. 1997, 79, 1945-1948). Fits deviate from the data when three different slopes were observed in the reptation plots. Reptation plots were used to determine a phase diagram for dsDNA migration regimes. The phase diagrams define different regions where mechanisms for molecular transport affect the migration of dsDNA in agarose gels during electrophoresis. The parameters from the equation have also been interpreted to provide a physical description of the structure of the agarose gel by calculating the pore sizes. The relations between the values for the pore sizes and the phase diagrams are interpreted to better understand the migration of the DNA through agarose gels.
Identifier: FSU_migr_etd-1207 (IID)
Submitted Note: A Dissertation Submitted to the Department of Physics in Partial FulfiLlment of the Requirements for the Degree of Doctor of Philosophy.
Degree Awarded: Fall Semester, 2002.
Date of Defense: October 23, 2002.
Keywords: DNA Electrophoresis, Agarose Gels, New Mobility, DNA Length Dependence
Bibliography Note: Includes bibliographical references.
Advisory committee: David H. Van Winkle, Professor Directing Dissertation; Randolph L. Rill, Outside Committee Member; Jianming Cao, Committee Member; Nicholas E. Bonesteel, Committee Member; Mark A. Riley, Committee Member.
Subject(s): Physics
Persistent Link to This Record:
Owner Institution: FSU

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Beheshti, A. (2002). DNA Electrophoresis in Agarose Gels: A New Mobility vs. DNA Length Dependence. Retrieved from