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Brian J. Kirby, PhD

Powerpoint Slides to Accompany Micro- and Nanoscale Fluid Mechanics: Transport in Microfluidic Devices . Chapter 14. Brian J. Kirby, PhD Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY. Ch 14: DNA Transport and Analysis.

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Brian J. Kirby, PhD

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  1. Powerpoint Slides to AccompanyMicro- and Nanoscale Fluid Mechanics: Transport in Microfluidic Devices Chapter 14 Brian J. Kirby, PhD Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY

  2. Ch 14: DNA Transport and Analysis • DNA is among the most important biomolecules to analyze • DNA in aqueous solution is also a prototype for linear polymers in good solvents • Idealized models can be used to predict DNA’s diffusive and electrophoretic transport, which collectively are inconsistent with the Nernst-Planck equation for transport of point ions • DNA is free-draining in electrophoresis and obeys Rouse dynamics • DNA is non-draining in diffusion and obeys Zimm dynamics

  3. Sec 14.1.1: Chemical Structure of B-DNA • DNA has a hydrophilic sugar (deoxyribose)backbonse with negatively charge phosphate groups and a sequence of nitrogenous bases (A, G, C, T) • DNA can melt (i.e. denature) and anneal (hydrogen bond) based on temperature and other solution factors • hydrogen bonding between DNA or RNA from two different sources is called hybridization

  4. Sec 14.1.2: Physical Properties of dsDNA • the physical properties of dsDNA are primarily a function of polymer contour length and solution conditions, but not base pair order • we model DNA physically as an idealized contour through space • geometric definitions for DNA include the diameter, radius of gyration, and persistence length

  5. Sec 14.1.2: Physical Properties of dsDNA • the coordinate system of a DNA polymer contour is defined using the arclengths from one end

  6. Sec 14.1.2: Physical Properties of dsDNA • thepersistence length is a measure of the rigidity of a linear polymer • the persistence length is evaluated by determining how quickly the orientation of a polymer backbone changes as we traverse the contour

  7. Sec 14.1.2: Physical Properties of dsDNA • the radius of gyration is a measure of the space taken up by the linear polymer • the radius of gyration is evaluated by calculating the time average of the root-mean-square distance of the polymer components from the centroid:

  8. Sec 14.2: DNA Transport • DNA diffuses as if it were a rigid sphere with a radius equal to about one third of the radius of gyration. • DNA behaves like a rigid sphere because viscous interactions are long range (i.e. they decay as 1/r) and the viscous connections between the polymer components are stronger than the viscous interaction of the DNA molecule as a whole with the surrounding fluid

  9. Sec 14.2: DNA Transport • unlike for diffusion, DNA’s electrophoretic mobility is independent of contour length for all but oligomeric DNA • DNA electrophoresis is independent of length because electrostatic interactions are short range (i.e. they decay as exp-r/λD) and the electrostatic connections between the polymer components are weak

  10. Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties • The Kratky-Porod or wormlike chain model describes DNA as if it were a beam with flexural rigidity YI

  11. Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties • The freely jointed chain model describes DNA as if it were a series of rigid rods connected by free ball joints • The joints are imagined to be of a length given by the Kuhn length lK

  12. Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties • The freely rotating chain model describes DNA as if it were a series of rigid rods connected by ball joints with fixed colatitudinal angle but free azimuthal angle (i.e. like an alkane polymer) • The joints are imagined to be of a length given by the Kuhn length lK

  13. Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties • The Gaussian bead-spring model modifies the freely jointed chain model to incorporate springs of finite stiffness. • This model leads to the simplest mathematical results • The joints are imagined to be of a length given by the Kuhn length lK

  14. Sec 14.4: Real Polymer Models for DNA • Idealized polymer models are only correct for DNA in theta solvents, for which the electrostatic DNA–solvent interaction is identical to the DNA–DNA interaction. • Idealized polymer models can describe only entropic interactions. • In a good solvent, such as aqueous solution, DNA acquires a negative charge and exhibits electrostatic interactions that dictate polymer conformation.

  15. Sec 14.5: dsDNA in Confining Geometries • DNA confined in a nanochannel is influenced by electrostatic (energetic) forces as well as confinement (entropic) forces. • DNA whose end-to-end length is controlled exhibits entropic spring behavior

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