Electric Birefringence Technique Research Articles

Electro-optical studies of conformation and interaction of polynucleotides.

AbstractMeasurements by the technique of electric birefringence with pulsed sinusoidal electric fields on polyriboadenylic acid (poly‐A) and polyribouridylic acid (poly‐U) indicate that the kinetics of the double‐stranded helix formation of poly (A + U) in the presence of Mg2+ is second order and consists of two steps: nucleation and propagation of base pairs from nuclei. The nucleation involves approximately 7 base pairs. It seems that the requirement of 7 base pairs to start the formation of a double‐stranded helix is not peculiar to poly (A + U) but is associated with double‐stranded helices of polynucleotides in general. This implies that it may be associated with spatial requirements of the phosphate‐sugar backbone, rather than with the particular bases linked to the backbone. The decline in rate of poly (A + U) formation observed above a critical temperature is the consequence of changes in the poly‐A conformation setting in at this critical temperature, rather than resulting from an increase in the reversibility of the base‐pair propagation step of double‐stranded helix formation. The dominant role of the conformation of poly‐A in the double‐stranded helix formation of poly (A + U) is further borne out by the pH dependence of the rate which completely parallels the conformation changes known to occur in poly‐A as a function of pH. This indirectly suggests that at neutral pH poly‐A is a single‐stranded helix. The rotary diffusion coefficients attest to the flexibility of this helix, while the stacked nature of the base pairs at low temperatures is revealed by the identical increments in the specific Kerr constant on going from poly‐A to poly (A + U) and from poly (A + U) to poly (A + 2U) helices. Results suggest that Mg2+ binds to the phosphate part of the backbone. Poly‐U binds Mg2+ more strongly than poly‐A; this difference in binding strength is attributed to differences in conformation (random coil versus helix). It is also borne out by the present results that the degree of order in the structure of poly‐U, even at low temperatures and neutral pH, is at best an order of magnitude smaller than that of poly‐A under similar conditions. Furthermore, the earlier proposed double‐stranded structure of poly‐U is called into question. A hairpinlike structure seems to agree with results of this investigation. Finally, the results support the contention that the ion atmosphere polarization is responsible for orientation of polyelectrolytes in the presence of alternating electric fields in the neighborhood of 25 kc./sec. frequency.