Linear dichroism demonstrates that the bases in poly[d(AC)] · poly[d(GT)] and poly[d(AG)] · poly[d(CT)] are inclined from perpendicular to the helix axis

Abstract

Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)].poly[d(GT)] and poly[d(AG)].poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines.

Infrared Linear Dichroism Reveals That A-, B-, and C-DNAs in Films Have Bases Highly Inclined from Perpendicular to the Helix Axis

“…Although our IR LD results do not have the information content to give specific inclination angles for individual bases, the angles do provide other important information about base orientation in the double-helical DNA structure. We , and several natural DNAs in aqueous solution using flow UV LD measurements (20-25°f or purines and 30-35°f or pyrimidines in B-DNA) (Kang & Johnson, 1993;Chou & Johnson, 1993). We also reported that A-DNA has slightly increased inclinations for both the purine and the pyrimidine bases.…”

“…However, Ovaska et al (1984) used a fixed partial charge model to calculate the transition dipole directions for the double-bond region vibrations of pyrimidine bases and reported that the band at about 1670 cm™1 is mainly the C2=0 stretching, and the band at about 1710 cm™1 is mainly due to C4=0 stretching of thymine. In addition, our earlier UV LD results (Kang & Johnson, 1993;Chou & Johnson, 1993) showed that the axis of inclination for the thymine base lies in the same direction as the transition dipole of the C4=0 bond stretching vibration. Since this band has the largest dichroic ratio we expect its transition dipole to be in the same direction as the axis of inclination, confirming the assignment of the band at about 1710 cm™1 to the C4=0 bond stretching vibration rather than C2=0 bond stretching vibration of thymine.…”

“…Figure 4 represents the dependence of on the inclination of the base, a, and direction of transition dipole relative to the axis of inclination in the base plane, ß. The directions of vibrational transition dipoles for the pyrimidine bases were calculated by Ovaska et al (1984), and the axes of inclination for each base are known from our UV LD measurements (Kang & Johnson, 1993;Chou & Johnson, 1993). It is obvious from Figure 4 that is more affected by the relative direction of the transition dipole with respect to the axis of inclination for more highly inclined bases.…”

“…In this study we apply IR LD measurements to synthetic polynucleotides poly [d(AC) ] -poly [d(GT)] and poly-[d(AG) ] -poly [d(CT)] and natural DNAs (from E. coli and calf thymus) in oriented films to extract inclination angles for the bases in the A, B-, and C-forms. We compare the IR LD results with our earlier UV LD results about base inclination in aqueous solution (Chou & Johnson, 1993;Kang & Johnson, 1993). In addition, since infrared spectroscopy is a very sensitive tool for monitoring the phosphodiester backbone ©…”

4',6-Diamidino-2-phenylindole (DAPI) interacts with rare structures of GC polymers

“…Moreover, it is known that the base pairs in the DNA molecule are not¯at but propeller twisted (Chou and Johnson 1993;Kang and Johnson 1993) and, since in the GC sequences stacking deformations are frequent, DAPI may ®nd a locally highly propeller twisted structure, where a partial intercalation, with its phenylindole chromophore moiety, can occur. In our model, DAPI can rotate to adopt a suitable geometry for insertion in the constrained GC sites that have the capacity to form an intercalation site to accommodate the extended bulky chromophore.…”