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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. - PowerPoint PPT Presentation
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© Cambridge University Press 2010
Brian J. Kirby, PhD
Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY
Powerpoint Slides to AccompanyMicro- and Nanoscale Fluid Mechanics: Transport in Microfluidic Devices
Chapter14
© Cambridge University Press 2010
• 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
Ch 14: DNA Transport and Analysis
© Cambridge University Press 2010
• 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
Sec 14.1.1: Chemical Structure of B-DNA
© Cambridge University Press 2010
• 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
Sec 14.1.2: Physical Properties of dsDNA
© Cambridge University Press 2010
• the coordinate system of a DNA polymer contour is defined using the arclength s from one end
Sec 14.1.2: Physical Properties of dsDNA
© Cambridge University Press 2010
• the persistence 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
Sec 14.1.2: Physical Properties of dsDNA
© Cambridge University Press 2010
• 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:
Sec 14.1.2: Physical Properties of dsDNA
© Cambridge University Press 2010
• 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
Sec 14.2: DNA Transport
© Cambridge University Press 2010
• 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
Sec 14.2: DNA Transport
© Cambridge University Press 2010
• The Kratky-Porod or wormlike chain model describes DNA as if it were a beam with flexural rigidity YI
Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties
© Cambridge University Press 2010
• 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
Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties
© Cambridge University Press 2010
• 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
Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties
© Cambridge University Press 2010
• 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
Sec 14.3: Ideal Chain Models for Bulk DNA Physical Properties
© Cambridge University Press 2010
• 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.
Sec 14.4: Real Polymer Models for DNA
© Cambridge University Press 2010
• 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
Sec 14.5: dsDNA in Confining Geometries
