ALBERT

Notes: The fluorescence intensity from randomly oriented, immobilized Rb. sphaeroides reaction centers at 77 K increases in the presence of an externally applied electric field. We have proposed that this increase is due to a net decrease in the rate of the forward electron transfer reaction which competes with the prompt fluorescence. This decrease results from the change in the free energy difference between the reactant and very dipolar product state in the presence of the electric field. Because the free energy change and thus the electron transfer rate for a given reaction center depends on its orientation relative to the field, the intensity of the competing fluorescence likewise becomes orientation dependent. An expression is derived relating the degree of this electric field induced fluorescence anisotropy to the angle ζet between the fluorescence transition moment and the effective dipole moment whose interaction with the field results in the change in the rate of the electron transfer reaction which competes with fluorescence. ζet is determined to be about 69°. This angle can be estimated from the x-ray crystal structure coordinates for possible identities of the initial electron acceptor. The results are inconsistent with a two-step hopping mechanism in which the bacteriochlorophyll on the L side is the initial electron acceptor whose formation competes with fluorescence. Effects of an electric field on the electronic coupling for a superexchange mechanism are discussed. The theoretical and experimental approach should be generally applicable for studying long-range electron transfer reactions.

Notes: Calculations of diffusion constants for rigid molecules of arbitrary shape are often based on hydrodynamic interactions between freely moving spheres. Molecules can be modeled as collections of spheres, and the interactions are approximated as pairwise additive. Singularities previously associated with nearly linear geometries and with geometries dominated by a large central element can be avoided by including torque-angular velocity and torque-velocity coupling, as well as the usual force-velocity coupling between spheres. I provide explicit formulas for these couplings for both nonoverlapping and overlapping spheres, and also show how to include effects of one sphere on the self-diffusion of another. This formulation is incorporated in an algorithm that involves neither Gauss–Seidel iterations nor direct inversion of a large matrix.

Notes: Seventeen DNA dumbbells were constructed that have duplex sequences ranging in length from 14 to 18 base pairs linked on the ends by T4 single-strand loops. Fifteen of the molecules have the core duplexes with the sequences 5′G-T-A-T-C-C-(W-X-Y-Z)-G-G-A-T-A-C3′, where (W-X-Y-Z) represents a unique combination of A · T, T · A, G · C, and C · G base pairs. The remaining two molecules have the central sequences (W-X-Y-Z) = A-C and A-C-A-C-A-C. These duplex sequences were designed such that the central sequences include different combinations of the 10 possible nearest-neighbor (n-n) stacks in DNA. In this sense the set of molecules is complete and serves as a model system for evaluating sequence-dependent local stability of DNA. Optical melting curves of the samples were collected in 25, 55, 85, and 115 mM [Na +], and showed, regardless of solvent ionic strength, that the transition temperatures of the dumbbells vary by as much as 14° for different molecules of the set.Results of melting experiments analyzed in terms of a n-n sequence-dependent model allowed evaluation of nine independent linear combinations of the n-n stacking interactions in DNA as a function of solvent ionic strength. Although there are in principle 10 possible different n-n interactions in DNA, these 10 are not linearly independent and therefore can not be uniquely determined. For molecules with ends, there are 9 linearly independent combinations, as opposed to circular or semiinfinite repeating copolymers where only 8 linear combinations of the 10 possible n-n interactions are linearly independent. The n-n interactions are presented as combinations of the deviations from average stacking for the 5′-3′ base-pair doublets, δGi, and reveal several interesting features: (1) Titratable changes in the values of δGi, with changing salt environment are observed. In all salts the most stable unique combination is δG4 = (δGGpC + δGCpG,)/2, and the least stable is the GpG/CpC stack, δG2 = δGGpG/CpC. (2) The χ2 values of the fits of the evaluated δGi's to experimental data increased with decreasing [Na +], suggesting that significant interactions beyond nearest neighbors become more pronounced, particularly at 25 mM Na +. (3) In 85 and 115 mM Na +, where the n-n approximation seems to be most valid, the absolute value of δGi for any n-n stack or average of two n-n stacks is not more than ∼ 220 cal/mole, indicating that deviations from average stacking due to n-n interactions represent about 15% of the total stability of a base pair. The overall thermodynamic stability of DNA is predominantly determined by the sequence content (%G · C). Even though the contribution of n-n interactions to overall stability are intrinsically small, reliable predictions of DNA transition temperatures de novo from sequence can be significantly compromised by cumulative errors in the δGi's. (4) Comparisons of our set of n-n linear combinations evaluated in 115 mM Na+ with various published sets evaluated from melting experiments of long restriction fragments, synthetic polymers, and short oligomers, and those obtained from a reanalysis of published melting data of synthetic polymers, are presented. The analysis reveals a major consensus agreement between n-n free energies evaluated from melting data of restriction fragments and long synthetic repeating copolymers. In contrast, only a minor consensus agreement is obtained between our n-n set and these values or those obtained from melting analysis of a combination of short oligomers and long polymers or those theoretically calculated. Results of these comparisons suggest the values of n-n interactions evaluated from DNA melting curves depend on the length of the melted duplex regions of the DNA molecules that comprise the sample set.

Notes: The diffusional motions of flexible macromolecules are analyzed with an increasingly realistic Rouse-Zimm model, i.e., by modeling the molecule as an arbitrary set of spheres connected by nearly harmonic springs. New features include (1) nearly arbitrary arrangements of spheres, (2) arbitrary arrangements of translational and torsional springs, (3) significant anharmonic corrections to the elastic potential surface, and (4) inclusion of torsional damping and various hydrodynamic cross-coupling effects (including two types of translational-rotational coupling) with no additional fitted parameters.The hydrodynamic interactions [R. F. Goldstein (1985) Journal of Chemical Physics, Vol. 83, pp. 2390-2397] contain no adjustable parameters other than temperature, viscosity, and the radii and positions of the spheres. These hydrodynamic interactions allow accurate calculations of rigid body diffusion as well as flexible motions.Given the positions, radii, and spring constant matrix, one can calculate a full set of three-dimensional diffusional modes. Because one uses an off-diagonal hydrodynamic resistance matrix instead of a diagonal mass matrix, the diffusional modes are different in structure from vacuum normal modes, and give rise to different rms motions in the laboratory frame. These hydrodynamic modes include the effects of vibrational-translational cross-coupling (i.e., motion along a vibrational coordinate may give rise to a translational force, and vice versa).The diffusional modes are used to simulate dynamic light scattering (DLS). I examine various molecules with different shapes, flexibilities, and with different scattering vectors. Radial and angular motions influence DLS decays differently. These effects are dependent upon the molecular shape (straight, bent, or curved) and type of flexibility (stretching or bending). Furthermore, small cubic corrections to the potential surface can be significant for DLS of certain geometries such as straight rods and semicircles. © 1993 John Wiley & Sons, Inc.

Notes: There are 10 unique dinucleotides of double-stranded DNA, but only 8 independent nearest-neighbor energies that occur in circular DNA, as shown by D. M. Gray and I. Tinoco [(1970) Biopolymers 9, 223-244]. We extend that analysis to include end effects, and show that the number of unique dinuoleotide pairs (including ends) is 14. but there are only 12 independent energies. We discuss how these 12 energies (or spectra or any other pairwise additive property) can be measured and displayed, and how they should and should not be compared between experimenters. As an example, we analyzed the recently reported melting curves [M. J. Doktycz et al. (1992) Biopolymers, 32, 849-864] of 16 DNA dumbbells in two different Na+ environments. This analysis reveals a new means for evaluating end effects and the emergence of longer than nearest-neighbor interactions at low salt concentration. © 1992 John Wiley & Sons, Inc.