DNA Elasticity with Transition

We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25–45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.

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DNA elasticity: topology of self-avoidance

Journal of Physics Condensed Matter ◽

10.1088/0953-8984/18/14/s10 ◽

2006 ◽

Vol 18 (14) ◽

pp. S253-S268 ◽

Cited By ~ 12

Author(s):

Joseph Samuel ◽

Supurna Sinha ◽

Abhijit Ghosh

Keyword(s):

Dna Elasticity

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Statics of DNA Deformations

Molecular Machines ◽

10.23943/princeton/9780691173863.003.0002 ◽

2018 ◽

pp. 25-80

Author(s):

Giovanni Zocchi

Keyword(s):

Nearest Neighbor ◽

Persistence Length ◽

Hamiltonian Formulation ◽

Experimental System ◽

Dna Elasticity ◽

Flexible Molecules ◽

Dna Yield ◽

Bending Modulus ◽

Linear And Nonlinear ◽

Linear And Nonlinear Elasticity

DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long DNA molecules are an excellent experimental system to study the equilibrium conformations and dynamics of long, flexible molecules. This chapter discusses the following: DNA melting, the zipper model, experimental melting curves, base pairing and base stacking as separate, Hamiltonian formulation of the zipper model, 2 × 2 model, nearest neighbor model, connection to nonlinear dynamics, linear and nonlinear elasticity of DNA, bending modulus and persistence length, measurements of DNA elasticity (short and long molecules), the Euler instability, and the DNA yield transition.

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