SynopsisThe conformational change of Li-DNA in water/ethanol mixtures is followed by the change in the CD spectrum in solutions containing various percentages of ethanol in the range from 0 to 95%. Two main transitions can be distinguished. The first occurs in the range from 0 to 70% and is represented by a large reduction of the intensity of the positive CD band around 275 nm, which is apparently related to a small change in the number of base pairs per turn. Secondly, at higher percentages of ethanol (> 80%) a conformational change is detected, which is expressed as a reduction of the 245-nm negative CD intensity. According to x-ray difiaction experiments of fibers of Li-DNA, the C-form is attained in 95% ethanol, while at 70% ethanol a B-like structure is observed. The CD experiments reported here also show that for DNA in solution the dependence on percentage of ethanol is composed of two main transition regions. The C-form would then be adopted at high (-958) ethanol percentage. The 670% transition, although strongly expressed in optical CD experiments, has to be related to relatively small structural changes within the B-family of DNA structures, which probably induce an enhanced contribution of n --t n* transitions to the CD spectrum.

SynopsisThe CD and absorption (OD) spectra of single-stranded nucleic acids in complex with the helix-destabilizing protein of either bacteriophage T4 (GP32) or bacteriophage fd (GP5) show similar and unusual features for all polynucleotides investigated. The change in the CD spectra between 310 and 240 nm is in all cases characterized by a considerable decrease in the positive band, while the negative band (if present) remains relatively intense. These changes are different from those due to temperature or solvent denaturation and, moreover, cannot be induced by the binding of simple oligopeptides. Absorption measurements show that all polynucleotides remain hypochromic in the complex. Both CD and OD spectra point to a specific and probably similar conformation in complex for all polynucleotides with substantial interactions between the bases. The spectral properties are almost temperature independent (0-40°C). Therefore, we conclude that the conformation must be regular and rigid. To investigate the relation between these optical properties and the specific polynucleotide structure, CD and OD spectra were calculated for an adenine hexamer over a wide range of the conformational parameters. It appears that the calculated CD intensity is not very sensitive to an increase in the axial increment and that many different conformations can give rise to more or less similar CD spectra. However, simulation of the very nonconservative experimental CD spectrum of the poly(rA)-GP32 complex requires that the conformation satisfies two criteria: (1) a considerable tilt of the bases (< -10") in combination with (2) a small rotation per base (=ZOO) andor a position of the bases close to the helix axis (dx = 0 A). Such conformations can also explain the observed hyperchromism upon binding of GP32 to poly(rA)/(dA). Very similar structural characteristics also account for the optical properties of the complexes with GP5. These are discussed as an alternative to the structure suggested by Alma-Zeestraten for poly(dA) in the complex [N. C. M. Alma-Zeestraten (1982) Doctoral thesis Catholic University, Nijmegen, The Netherlands]. The secondary structure proposed in this work can be reconciled with the overall dimensions of the complex, assuming that the polynucleotide helix is further organized in a superhelix.

Calf thymus DNA was modified with 2-aminofluorene (AF) to different extents by treatment with N-hydroxy-2-aminofluorene. The AF-modified DNAs together with free AF, the AF-modified guanine (Gua-C8-AF) and the AF-modified deoxyguanosine (dGuo-C8-AF) were subsequently studied by u.v. absorbance, linear dichroism and fluorescence spectroscopy. The emission and absorption properties of double-stranded DNA-AF and single-stranded DNA-AF closely resemble those of dGuo-C8-AF. The emission spectra of these three compounds show a broad, red-shifted emission, characteristic for exciplex formation. The linear dichroism and circular dichroism spectra of double-stranded DNA-AF show that the AF moiety forms a well-defined, regular structure. The dichroic ratio in the 310-340 nm region is constant, which indicates the presence of only one type of adduct. The long-wavelength transition moment of this adduct makes an angle of 72-74 degrees with the DNA helix axis. The binding of AF to double-stranded is DNA is accompanied by a destabilization of the DNA helix structure, a strong quenching of the AF emission quantum yield, intense AF circular dichroism and an apparent immobilization of the dGuo-C8-AF complex. In single-stranded DNA-AF, the AF conformation appears more random, although the interactions between AF and the surrounding bases persist. The strong interactions between AF and the surrounding bases which dominate the optical properties of the studied complexes, the significant destabilization of the DNA double helix after modification with AF, and the relatively small angle between AF and the base planes support a model in which the adduct is inserted into the DNA helix.