Low‐frequency dynamics and Raman scattering of crystals, of B‐, A‐, and Z‐DNA, and fibers of C‐DNA

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Abstract
Normal modes of vibration of DNA in the low-frequency region (10–300 cm−1 interval) have been identified from Raman spectra of crystals of B-DNA [d(CGCAAATTTGCG)], A-DNA [r(GCG)d(CGC) and d(CCCCGGGG)], and Z-DNA [d(CGCGCG) and d(CGCGTG)]. The lowest vibrational frequencies detected in the canonical DNA structures—at 18 ± 2 cm−1 in the B-DNA crystal, near 24 ± 2 cm−1 in A-DNA crystals, and near 30 ± 2 cm−1 in Z-DNA crystals—are shown to correlate well with the degree of DNA hydration in the crystals structures, as well as with the level of hydration in calf thymus DNA fibers. These findings support the assignment [H. Urabe et al. (1985) J. Chem. Phys. 82, 531–535; C. Demarco et al. (1985) Biopolymers 24, 2035–2040] of the lowest frequency Raman band of each DNA to a helix mode, which is dependent primarily upon the degree of helix hydration, rather than upon the intrahelical conformation. The present results show also that B-, A-, C-, and Z-DNA structures can be distinguished from one another on the basis of their characteristics Raman intensity profiles in the region of 40–140 cm−1, even through all structures display two rather similar and complex bands centered within the intervals of 66–72 and 90–120 cm−1. The similarity of Raman frequencies for B-, A-, C-, and Z-DNA suggests that these modes originate from concerted motions of the bases (librations), which are not strongly dependent upon helix backbone geometry or handedness. Correlation of the Raman frequencies and intensities with the DNA base compositions suggests that the complex band near 90–120 cm−1 in all double-helix structures is due to in-plane librational motions of the bases, which involve stretching of the purine-pyrimidine hydrogen bonds. This would explain the centering of the band at higher frequencies in structures containing G ⃛ C pairs (> 100 cm−1) than in structures containing A ⃛ T pairs (< 100 cm−1), consistent with the strengths of G ⃛ C and A ⃛ T hydrogen bonding.