Proton NMR and circular dichroism studies of the B and Z conformations of the self-complementary deoxyhexanucleotide d(m5C-G-C-G-m5C-G): mechanism of the Z-B-coil transitions

Abstract

The double-helical conformations of d(m5-C-G-C-G-m5-C-G) in aqueous solution were studied by circular dichroism and 1H NMR spectroscopy. In 0.1 M NaCl, only the B form is detected whereas the Z form is strongly predominant in 3 M NaCl. In the presence of 2 M NaCl, two resonance signals corresponding to the B and Z duplexes were observed for each proton below 50 degrees C, indicating a slow exchange between B and Z. However, the B-Z exchange becomes intermediate or fast in the 55-80 degrees C temperature interval. By contrast the exchange between B helix and single-stranded (or coil) forms is much faster for the same temperature conditions. The Z form is only detectable when the coil form is practically absent. With decreasing temperature the B form decreases in favor of the Z form. From proton line-width measurements under various experimental conditions, it was also shown that Z exchanges only with B, while the latter also exchanges with the single-stranded form (S): Z in equilibrium B in equilibrium S. The enthalpy value is about 8 +/- 1 kcal/mol for the B-Z transition and about 40 +/- 2 kcal/mol for the B-S dissociation (2 M NaCl solution). The activation energy is about 47 +/- 2 kcal/mol for the Z----B and 39 +/- 2 kcal/mol for the B----Z reaction. Very good agreement between the experimental results and computed data (based on the above kinetic reaction model) was found for the B, Z, and coil proportions. The B-Z transition of methylated d(C-G)n oligomers is only possible when the Watson-Crick hydrogen bonds between the CG base pairs are firmly maintained; otherwise, the transformation from B to Z would not occur, and B-S dissociation would take place instead.

Proton NMR study of the B–Z transition of d(CGm5CG)2and d(CGm5CGCG)2: theory and experiment

“…For the base protons the experimental results show that the CH protons of the cytosines are shifted upfield while smaller shifts are measured, on the average, for H8 of guanine (6,7). This clearcut difference between the two types of base is very well given by the calculations.…”

“…Although the degree of purity, in solution, of the Z conformation of the riboses could not be determined, because of the line widths and resonance overlaps (6,7) which prevent the measurement of the coupling constants, we can reasonably suppose that in this case the situation is analogous to that occuring in low salt solution and that the duplexes do not have a perfect regular Z-DNA conformation. This hypothesis is supported by the fact that the values of da obtained for the four different Z-DNA geometries can vary for a sam proton by 0.7 ppm a value which is much larger than the differences experimentaly measured between the four duplexes studied in high salt solutions (see Table 1 and 2 and ref.…”

“…The B and Z forms can also be observed simultaneously at intermediate salt concentrations between 1.5 -2.0 X NaCl. The proton assignments for the B Form were performed by the methods described elsewhere (6,7,16). The Z proton resonances were assigned using the polarization transfer (in 1.5 -2 N NaCl solutions) and proton-proton decoupling (at high salt concentration) methods.…”

Characterization of DNA structures by infrared spectroscopy: double helical forms of poly(dG-dC)•poly(dG-dC), poly(dD8G-dC)•poly(dD8G-dC), and poly(dG-dm5C)•poly(dG-dm5C)

“…Their existence has been definitively proved by X-ray diffraction studies on d(C-G)3 crystals (2). Nuclear magnetic resonance (nmr) (3,4) and Raman spectroscopy (5-9) have also been used to investigate Z DNA. Thamann et al (6) showed that the Raman spectrum of the Z DNA d(C-G), crystal is essentially identical to the high salt solution spectrum of poly(dG-dC).poly(dG-dC).…”

Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments

“…Recent studies on d(m5C-G-C-G-m5C-G) [5], d(C-Gm5C-G-T-G) [6] and d(m5C-G)3 [7] have shown that short oligomers are very suitable models to study the B P Z transition in solution by 'H-NMR spectroscopy. Following this work, we examine here the influence of the replacement of two dC and dG residues by dT, dA or d(2aminoA) in alternating d(C-G), oligonucleotides on this structural transition.…”