The nature of "unusual" electro-optical transients observed for DNA

On the possibility of the existence of orienting hydrodynamic steering effects in the kinetics of receptor-ligand association

In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of the ligand relative to the binding site. Before the formation of the initial form of the complex, only long-range, electrostatic and hydrodynamic interactions can act between the ligand approaching the binding site and the receptor. In this context, the question arises whether as a result of these interactions, there is a pre-orientation of the ligand towards the binding site, which to some extent would accelerate the formation of the complex. The role of electrostatic interactions in the orientation of the ligand relative to the binding site of the receptor is well documented. The analogous role of hydrodynamic interactions, although assessed as very significant by Brune and Kim (PNAS 91, 2930-2934, (1994)), is still debatable. In this article, I present the current state of knowledge on this subject and consider the possibilities of demonstrating the orienting effect of hydrodynamic interactions in the processes of receptor-ligand association, in an experimental way supported by computer simulations.

Structures during binding of cAMP receptor to promoter DNA: promoter search slowed by non-specific sites

The kinetics of cAMP receptor (CAP) binding to promoter DNA has been studied by stopped-flow electric-dichroism at a reduced salt concentration, where the coupling of non-specific and specific binding can be observed directly. Amplitudes, rise and decay times of dichroism transients provide detailed information about the reaction and the structure of intermediates over more than six orders of magnitude on the time scale. CAP binding during the first milliseconds after mixing is indicated by an increase of both rise- and decay-time constants. A particularly large increase of rise times reflects initial formation of non-symmetric complexes by protein binding to non-specific sites at DNA ends. The increase of the hydrodynamic dimensions continues up to ~1 s, before a decrease of time constants reflects transition to compact states with bent DNA up to the time range of ~10(3) s. The slow approach to CAP-induced DNA bending is due to non-specific complexes, which are formed initially and are converted slowly to the specific complex. At the salt concentration of 13.5 mM, conversion to specific complexes with bent DNA is completed after ~40 s at pH 8 compared to >10(3) s at pH 7, resulting from a higher affinity of CAP to non-specific sites at pH 7 than 8 by a factor of ~100. Thus, under the given conditions non-specific sites delay rather than facilitate formation of the specific complex with bent DNA. Experimental data obtained for a non-specific DNA clearly indicate the impact of pseudo-sites. The different electro-optical parameters have been combined in global fits.

Electric birefringence at small angles from crossed position: enhanced sensitivity and special effects

Measurements of electric birefringence with increased sensitivity are possible using lasers with high intensity and stability, provided that perturbations resulting from stray light and strain in cell windows can be reduced. A new type of cell window is designed for minimal strain and is used in a standard birefringence setup with optimized components. The new instrument is characterized by a stray-light constant of 2 × 10(-7) and a negligible residual birefringence. Thus, measurements can be extended to small angles from the crossed position providing birefringence signals of high amplitudes at favorable signal-to-noise ratios. Special effects at small angles from the crossed position like a divergent increase of relative amplitudes to extreme values, a nonlinear response, a new type of electro-optical anomaly, and a simple bypass around this anomaly are observed and shown to be consistent with the theory. The technique proves to be particularly useful for measurements at physiological salt concentrations, where signals for most systems are too small under conventional conditions.

Field-induced alignment of flexible polyelectrolytes in solution

Molecular dynamics simulations are used to study dynamical coupling between conformational fluctuations of a highly charged flexible macromolecule and its surrounding ionic cloud. We find that the basic model of a polyelectrolyte as a chain of charged monomers captures the main experimental findings on the field-induced alignment of polyelectrolytes despite its simplicity. Contrary to current theories, the correlated local charge and field fluctuations in the vicinity of the macromolecule are found to dominate alignment along an external field. We suggest that short-lived monomer-counterion clustering can be probed by measuring the field-induced anisotropy of x-ray and neutron scattering from polymer solutions.

Unique Physical Signature of DNA Curvature and Its Implications for Structure and Dynamics

A particularly sensitive birefringence technique is used to analyze a curved DNA fragment with 118 bp and a standard DNA with 119 bp. At salt concentrations from 0.5 to 10 mM, both fragments show the usual negative stationary birefringence and monotonic transients - differences are relatively small. At 100 mM salt the curved DNA shows a positive stationary birefringence and non-monotonic transients with processes having amplitudes of opposite sign, whereas signals of the standard DNA remain as usual. Transients induced by reversal of the field vector indicate the existence of a permanent dipole for the curved DNA. 2-MHz-ac pulses induce a negative stationary birefringence in both DNAs. These results are consistent with calculations on models for curved DNA predicting a quasi-permanent dipole and a positive dichroism/birefringence. The quasi-permanent dipole results from the loss of symmetry in the charge distribution of the curved polyelectrolyte. The appearance of the unique signature of curvature at high salt is mainly due to a strong decrease of the polarizability by about 2 orders of magnitude. The special mode of orientation resulting from the quasi-permanent dipole is expected to contribute to the gel migration anomaly. The time constants of birefringence decay for the curved fragment are shorter than those of the 119 bp fragment by a factor of approximately 1.10 at 0.6 mM salt, whereas this factor is approximately 1.20 at 100 mM Na+. If both fragments were normal DNA with 3.4 A rise per base pair, the factor would be approximately 1.02. At high salt and high electric field strengths the factor increases up to 1.37. The implications for the bending dynamics and the potential to distinguish static from dynamic persistence by field reversal experiments are discussed. The dependence of the curvature on the salt concentration indicated by the time constants is consistent with a clear decrease of the electrophoretic anomaly at decreasing salt concentration.