Opticohydrodynamic properties of high‐molecular‐weight DNA. III. The effects of NaCl concentration

Abstract

SynopsisExcluded volume and persistence length of high-molecular-weight DNA from T2 bacteriophage have been evaluated over a range of NaCl concentrations from 0.005 to 2.0M using low-shear flow-birefringence and intrinsic-viscosity data. Uncertainty in persistence length due to ambiguity in the assignment of intrinsic birefringence has been avoided by calibrating the data at 0.2M NaCl using a recently reported persistence-length value based upon photon that the combined flow-birefringence-intrinsic-viscosity technique employed here may be more sensitive to the distribution of chain stiffness and excluded volume in polyelectrolyte chain expansion of DNA than are other hydrodynamic methods such as sedimentation or intrinsic viscosity alone.

A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations

“…For the case where d≠2 and ξ>1 nt, similar steps used to obtain Equation (18) yield a general expression (for d>0, g>0, and 0<n<1) (20) where, v=(g+1/d)/z(g,d) is a stretching weight on the gamma function, and in general, we assume D=3. When d≡2, then v≡1 and Equation (20) reduces to Equation (18).…”

“…If the Kuhn length is variable over the length of the sequence, then we suppose that the sum of the individual Kuhn lengths (ξi) should equal the total number of monomers, i.e., (24) This suggests that we can write Equation (20) as a summation (25) Simplifying Equation (25) to a form like Equation (18) yields (26) For the limiting case of large xi, the local FE approaches (27) and using Equation (24), it is clear that the total free energy caused by this entropy change is again approximately (g+1/2)NkBT/D. Hence, the model easily adapts to a more general expression with little difficulty.…”

“…This fact allows us to suppose two distinct Kuhn lengths: one for loops (ξL) and one for stems (ξs). Now we suppose that the constant (A JS ) in the JS expression comes from the renormalization constant (DGξ /Ñ): introduced in Equation (18) and Equation (20) as applied to a generic stem-loop structure (42) where is the derived JS constant (A JS ), becomes the average stem length and is the average loop length of the generic RNA stemloop structure. The factor of two in Equation (42) is from the fact that the two independent single-stranded parts of the chain must join together to form the double-stranded helix of the RNA stem and each segment achieves this new Kuhn length independently.…”

“…Experimental work has also focused on the effects of ionic strength. [16][17][18][19][20] With the development of atomic force spectroscopy (AFM) and related deposition experiments, the persistence length has been measured based on the curvature of the DNA on a 2D planar surface under various conditions. [21][22][23] Numerous studies of dsDNA using optical tweezers in force extension experiments report the persistence length.…”

A new entropy model for RNA: part I. A critique of the standard Jacobson-Stockmayer model applied to multiple cross links

“…In unstressed equilibrium experiments, the typical Kuhn length of dsDNA or dsRNA is quite long; about 50 to 200 bps. [80][81][82][83] Pulling experiments on ssDNA and ssRNA tend to be very flat until near maximum extension, [84][85][86] characteristic of a fairly long Kuhn length. However, in Figure 7, the rise of this hdsRD polymer is more characteristic of ssRNA or ssDNA.…”