Calculated CD Spectra Research Articles

Circular dichroism calculations for double‐stranded polynucleotides of repeating sequence

AbstractOptical property calculations are presented for poly(A·U), poly[(A‐U)·(A‐U)], poly(G·C), and poly[(G‐C)·(G‐C)] in RNA, B‐DNA, and C‐DNA conformations. An all‐order classical coupled oscillator polarizability theory was used, and an effective dielectric constant of 2 was assumed. The calculated CD spectra were found to be sensitive to both geometry and sequence. Agreement with the measured CD spectra of poly(A·U), poly(G·C), and poly(dG·dC) is very good. Calculations for other sequences and geometries are less satisfactory and are particularly poor for poly[(G‐C)·(G‐C)] in RNA geometry and poly(A·T) in B‐DNA geometry. Attempts to improve agreement with measured spectra by varying monomer properties have been only partially successful for these calculations, but they illustrate the types of changes that may prove to be necessary. Calculations using other published X‐ray coordinates for certain deoxypolynucleotides of simple sequence, some of which are quite different from B‐DNA coordinates, did not result in better agreement with measured spectra. Finally, the dependence of the calculated CD on chain length is examined. Results show that non‐nearest neighbor interactions can be important when runs of 3 or more identical base pairs appear in a given sequence.

Cicular dichroism of hapten-antibody complexes: Calculation of the interaction of a trinitrophenyl hapten with tryptophan

The circular dichroism resulting from the interaction of a trinitrophenyl moiety of Tnp-aminocaproate and an indole chromophore of tryptophan was calculated using the Kuhn-Kirkwood dynamic coupling mechanism and the point dipole approximation for the potential energy of interaction. For some geometries, in which the two chromophoric groups lie close to each other but are not necessarily parallel, the calculated CD spectra display the variation in magnitude and sign of observed circular dichroic bands which occur upon the binding of Tnp haptens to different anti-Tnp antibodies. The data strengthen the argument for the interaction of tryptophan(s) in or near the antibody combining site of the MOPC-315 IgA myeloma protein with non-covalently bound Dnp- or Tnp-haptenic chromophores (Rockey et al., 1972; Freed et al., 1976). The data also indicate that tryptophanyl involvement in the antibody combining site may be a feature common to many anti-Tnp antibodies.

Conformational induction in copolypeptides of the form AnBm.

AbstractThe polymerization kinetics and optical rotatory properties of AnBm polypeptides have been studied, where A = D,L‐Tyr, D,L‐TyrZ, D,L‐LysZ, L‐AspOBzl, or L‐Asp‐ONBzl, and B = D,L‐GluOR (R = Me or Bzl). In most cases where An and Bm prefer the same helix sense, the polymerization of A N‐carboxyanhydride (initiated by Bm in dioxane) shows first order kinetics and produces a monotonic change in optical rotation, while if opposite helix senses are preferred, the kinetics are multiphasic and the change in rotation reverses direction after the addition of several residues. The rotation change in the latter case is interpreted to mean that the helix in the A block is initially induced to take the nonpreferred sense, as originally suggested by Doty and Lundberg from similar observations on (D‐GluOBzl)n‐(L‐GluOBzl)m. It is found here that the CD spectra for the latter polymer show the sign changes required by this hypothesis. The optical rotation curves and CD spectra for (D,L‐Tyr)n‐(L‐GluOBzl)20 suggest, by analogy, that (L‐Tyr)n prefers the same helix sense as (L‐GluOBzl)n. However, it is found that the opposite conclusion is equally consistent with the data if one considers the effects of possible changes in side‐chain conformation on these data in accordance with the calculated CD spectra of Chen and Woody. The optical rotation curves for (D‐GluOBzl)n‐(L‐GluOBzl)20, (D‐Tyr)n‐(L‐GluOBzl)20, and (L‐Tyr)n‐(L‐GluOBzl)20 are all found to be consistent with a two‐state equilibrium model in which the A block initially takes on an induced conformation and has an increasing tendency to revert to its preferred conformation as n increases. It is concluded that in both D‐Tyr and L‐Tyr the side‐chain and/or the backbone conformation is induced by the neighboring L‐GluOBzl block, and the data do not distinguish which type of change is occurring. These results are discussed in connection with other observations bearing on the helix sense of (L‐Tyr)n.