Marcos F. Maestre

Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films—A preliminary study

The circular dichroism and absorbance spectra of both oriented and unoriented DNA films (Escherichia coli and calf thymus DNAs) were studied as a function of salt of the nucleic acid (sodium and lithium), salt ion concentration and the relative humidity (100% hydrated down to 34% r.h.†). At 92% or higher humidities sodium and lithium salts of sheared or sonicated E. coli and calf thymus DNA showed a CD spectra that was essentially the same as that of the nucleic acids in solution. Presumably these films are of the DNA in the B form. At humidities in the range of 75 to 66% r.h. films with 3% sodium content by weight showed a CD spectra very similar to that of double-stranded RNA in solution or the A form geometry. However, LiDNA at low humidity showed a different CD spectra in which the positive 275 nm peak disappears and which shows similarities with the CD spectra of DNA solutions in which the salt concentrations are in the range of 4 to 6 m for both NaCl and LiCl. This type of spectra is presumably a C form geometry type. The calf thymus DNA at low humidities and low sodium ion concentrations shows very high magnitude ellipticities and a non-conservative type CD spectrum which is probably due to aggregation artifacts or strong optical interaction between close packed molecules in the film. In the case of the oriented DNA films it is shown that the CD spectra obtained, which shows a very high angular dependence as the film is rotated about the axis of the beam, can be interpreted as the sum of two components. By the use of Jones matrix calculus a general formula is developed which gives the apparent CD spectra of films having both linear and circular dichroism and linear and circular birefringence. For films that are reasonably thin and are only partially oriented these formulas reduce to a particularly simple form, the sum of the actual circular dichroism term plus a linear dichroism component which is a function of the orientation of the fast axis of the oriented DNA film with respect to the CD apparatus parameters. Using the formula, both the CD spectra and a linear dichroism spectra are obtained giving an insight into the orientation of the optical transitions of the DNA as it is found in the film. These equations give evidence for the possible existence of an n−π∗ transition below 240 nm and probably centered at 225 nm.

Optical rotatory dispersion of viruses.

The optical rotatory dispersion spectra of the following 16 viruses were measured: T2, T2(gt), T4, T6, T6(gt), λc, λ(K), λ(C), X174, T5, T7, B3, MS2, f2, R17 and α. T2 ghosts and T2, λ(C), λ(K), T7 and X174 DNAs and R17 RNA were also measured. The effect of high concentrations of lithium chloride salts at neutral pH on the DNA molecule in solution was also studied in relation to the packing of the DNA into the head of bacteriophages. The influence of the protein coat on the optical rotatory dispersion is shown to be small in the region above 250 mμ for DNA viruses of high nucleic acid content (∼50%), and for those viruses with nucleic acid content of around 25 to 30%; it is small above 280 mμ. The optical rotatory dispersion spectra of different types of viruses are qualitatively and quantitatively different. However, a difference spectrum of the nucleic acid inside and outside the virus shows qualitative similarities among all the DNA viruses tested. This indicates that the packing of the nucleic acid inside the virus has a common characteristic. Furthermore, the optical rotatory dispersion of the intact phage cannot be explained as the simple sum of the optical rotatory dispersion of the nucleic acid plus that of the protein coat. But the optical rotatory dispersion of osmotically shocked phage can be obtained by summing the optical rotatory dispersion of the DNA plus that of the ghost in solution. Equations are developed relating the different components of phage structure with the optical rotation spectra of the virus.

Self-assembly of porphyrins on nucleic acid templates

The cis and trans isomers of dicationic bis(4-N-methylpyridyl)diphenylporphine show a much greater tendency to aggregate than similar tetracationic porphyrins. Upon binding to nucleic acids these aggregating dicationic porphyrins form long-range structures on the polymer template giving intense circular dichroism signals whose profile reports the helical sense of the DNA.

Circular intensity differential scattering of light by helical structures. I. Theory

General expressions for the fields and intensities of scattered electromagnetic radiation by helical structures whose optical properties are described by a uniaxial polarizability along the tangent to the helix are obtained. Analytical expressions for the circular intensity differential of scattering (CIDS) as a function of the helix parameters and the wavelength of light are derived. It is shown that a sufficient condition for the existence of differential scattering for right and left circularly polarized light is the existence of an asymmetric polarizability. The choice of a uniaxial polarizability is found to give rise to form CIDS. For incident plane‐polarized light, the scattered fields are found to be generally elliptically polarized. The Stokes parameters describing the state of polarization of the scattered radiation are derived. These results are expected to be relevant both as a new method to characterize chiral regions in macromolecular structures as well as to describe the light scattering pr...

The psi‐type circular dichroism of large molecular aggregates. III. Calculations

Computations have been carried out to determine how the magnitude and shape of the polymer and salt induced (psi)‐type CD spectra depend on the structural properties of a collection of randomly oriented large chiral aggregates. Uniaxial polarizable groups located at the cubic lattice points have been used to model the aggregates. The structure of the model is similar to that of a cholesteric liquid crystal. All computations have been carried out for the case of polarizable groups possessing only one electronic transition between 200 and 320 nm. It is found that the radiation and intermediate couplings between the chromophores in the aggregate which are neglected in previous theories play an important role in determining the shape and magnitude of the psi‐type CD spectrum. It is shown that when these couplings are included, only three‐dimensional large chiral aggregates show huge and nonconservative psi‐type CD spectra. It is shown that the magnitude of the psi‐type CD spectrum is controlled by the volume,...

Circular intensity differential scattering of light. IV. Randomly oriented species

The theory of circular intensity differential scattering (CIDS) of light by a solution of randomly oriented molecules of arbitrary geometry has been derived. The molecules are treated as a set of polarizability tensors. The CIDS as a function of scattering angle is obtained in closed form. The CIDS depends on the distances and angle between all the polarizabilities in the molecule. Numerical calculations of helices made up of uniaxial polarizabilities, directed along the tangent to the helix, are shown as a function of helix geometry. The calculated values of the CIDS indicate that they should provide a useful, new experimental technique to determine the structures of biomolecular aggregates.

Circular intensity differential scattering of light by helical structures. II. Applications

Analysis and numerical calculations were made of the total scattering and differential scattering of circularly polarized light by helices as models of chiral structures. The differential scattering patterns are much more sensitive than the total scattering to helical parameters. For large helices the angular dependence of these patterns show lobes which alternate in sign. The number of lobes and the positions of the zeros directly measure the ratios of radius and pitch to wavelength. The signs depend on the sense of the helix. The results are compared with measured circular intensity differential scattering of membranes from the bacterium Spirillum serpens. Good qualitative agreement is obtained.

Differential scattering (CIDS) of circularly polarized light by dense particles

The circular intensity of differential scattering (CIDS) for structures composed of an arbitrary collection of point polarizable groups has been obtained in analytical form using the second Born approximation, both for oriented and rotationally averaged structures. It is found that: (i) A CIDS signal is present in the forward direction parallel to the light beam. This forward CIDS does not appear in CIDS patterns calculated using the first Born approximation alone; (ii) the magnitude and shape of CIDS patterns for oriented periodic structures depend only on the properties of one unit cell of the structures and are independent of the overall size; (iii) CIDS can exist for scatterers made up of a collection of spherically symmetric point polarizable groups. In the first Born approximation anisotropic polarizable groups are required for the CIDS to be different from zero. In the second Born approximation the anisotropy necessary for CIDS is generated by the interaction between the scattering groups; (iv) the CIDS is largest when the chiral dimensions of the scatterer are of the order of the wavelength of light.

Circular intensity differential scattering of light by helical structures. III. A general polarizability tensor and anomalous scattering

Numerical calculations of the circular intensity differential scattering of light by oriented helical structures made of units with general polarizability tensors are presented. The effects on the scattering patterns of both absorptive and dispersive properties of the units are illustrated. The differential scattering and the total scattering both show anomalous scattering phenomena; the differential scattering pattern is asymmetric when the wavelength of incident light is within an absorption band. Equations for biaxial polarizabilities are used to derive the symmetry properties of the differential scattering pattern and to show how this symmetry can be used to determine the right‐ or left‐handed sense of the helical structure. The wave‐length dependence of the scattering pattern is obtained for a Lorentzian polarizability.

Imaging differential polarization microscope with electronic readout

A differential polarization microscope forms two images: one of the transmitted intensity and the other due to the change in intensity between images formed when different polarizations of light are used. The interpretation of these images for linear dichroism and circular dichroism are described. The design constraints on the data acquisition systems and the polarization modulation are described. The advantage of imaging several biological systems which contain optically anisotropic structures are described.