Experimental Analysis of Superlooping in Twisted Polymer Line and its Applications to Mathematical Models of DNA

Experimental Analysis of Superlooping in Twisted Polymer Line and its Applications to Mathematical Models of DNAMarlen Mahendraratnam and Allison StillerBiomedical Engineering 16Advisor: Professor Stephen J. Burns University of Rochester Undergraduate Symposium-April 10th 2015

BackgroundDNA structure: double helix, four base pairs, linked with sugar and phosphate groups[1]Micron sized cell contains three meters of DNA[2]Superlooping: a mechanism to relieve strain energy

BackgroundSuperlooping affects gene expression and protein production[3,4,5,6]Nano-torsional/extensional testing for characterization of mechanics of superloopingMathematical models of superlooping

Fester, T. Beyond the Double Helix. http://www.scivit.de/blog/wp-content/uploads/2010/07/test7b.jpg

Strick, T. Biomolecular Nanomanipulation. http://www.ijm.fr/en/research/research-groups/biomolecular-nanomanipulation/

Transcription studies using Magnetic Tweezers(A) A DNA molecule is bound to a glass surface on one side and a magnetic bead on the other.(B) The DNA is twisted by turning a pair of magnets above the sample.(C) When an RNA polymerase molecule attaches to the promoter and unwinds the double helix, tensions decrease and the DNA extension increases.

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Our Goalverify the equations provided by Terrence Strick via torsional tests on an homogenous 50 lb fishing line Primarily, we are investigating the relationship between:applied twist (turns per unit length)applied force radius of the first resultant superlooplength of the polymer lineresearchers can better direct future mechanical testing of DNA

Equations Analyzed

Experimental Methods50 lb polypropylene fishing line Instron test frame with a load cell tensile test the elastic modulus of the polymer linefour sets of masses of 0.06lb, 0.16lb, 0.26lb, and 0.36lb Using Excel and MATLAB, graphs were created to show the relationships between L0 and twist, radii, L1, and L2

Video

Twist(Turns/Length) vs Original Length

Radius of First Superloop vs Original Length

Length at First Superloop vs Original Length

Length After Unwinding vs Initial Length

Comparison of Each Test By Applied Mass

Comparison of Theoretical and Experimental Radii

Rc,b= (B/2F)1/2

ConclusionsRelationship between twist at first superloop and original length: y=Axb. Linear relationship between original length, L0, and the final length, L2: y=mx+b. Radius of first superloop: experimental (our data) vs theoretical results (values found from equation) differ by a factor of 1.3

Future DirectionsFocus on both the application and removal of twistThis will provide more information on the nature of hysteresisCompare size of first loop of buckling to the sizes of the other loops formedWe noticed a ratio of about 1:4 and would like to explore this phenomena in greater detailClosed loop superloop formation (DNA plasmids)

Coleman, B. D., Swigon, D. , 2000.Theory of Supercoiled Elastic Rings with Self-Contact and Its Application to DNA Plasmids. Journal of Elasticity. 60: 181.

AcknowledgementsStephen J. Burns Ph.D.Christine Pratt, Senior Technical Associate

References [1] Strick, T., Allemand, J., Croquette, V., Bensimon, D. 2000. Twisting and stretching single DNA molecules. Progress in Biophysics and Molecular Biology. 74: 115-140.[2] Strick, T.R., Allemand, J.F., Bensimon, D., Croquette, V., 1998. Behavior of Supercoiled DNA. Biophysical Journal. 74: 2016-2028.[3]Hatfield, G.W., Benham, C.J., 2002. DNA Topology-Mediated Control of Global Gene Expression in Escherichia Coli. Annual Review of Genetics. 36: 175-203. [4] Gilbert, N., Allan, J., 2014. Supercoiling in DNA and chromatin. Current Opinion in Genetics and Development. 25:15-21.[5] van Loenhout, M. T. J., de Grunt, M.V., Dekker, C., 2012. Dynamics of DNA Supercoils. Science. 338:94-97.[6] Mosconi., F., Allemand, J. F., Bensimon, D., Croquette, V., 2009. Measurement of the Torque on a Single Stretched and Twisted DNA Using Magnetic Tweezers. Physical Review Letters.

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