B,Z Conformations and Mechanism of the Z-B-Coil Transitions of the Self-Complementary Deoxy-hexanucleotide d(C-G-m⁵C-G-C-G) by¹H-NMR and CD Spectroscopy

Abstract

The helical structures of d(C-G-m5C-G-C-G) were studied in aqueous solution at various salt concentrations and temperatures by CD and 1H-NMR spectroscopy. At room temperature only the B form is observed in 0.1 M NaCl whereas the B and Z forms are simultaneously present in 1.8 M NaCl. At high salt concentration (4 M NaCl) the Z form is largely predominant (greater than 95%). The Z form proton resonances were assigned by using the polarisation transfer method (between B and Z at 1.8 M NaCl) and by proton-proton decoupling (at high salt concentration). The Z-B-Coil transitions were studied as a function of temperature with the 1.8 M NaCl solution. At high temperature (95 degrees C) only the coil form (S) is present. Below 55 degrees C the coil proportion is negligible, and the B-Z exchange is slow. The disappearance of the coil gives rise at first to the B form and on lowering the temperature the Z proportion increases to the detriment of the B form. Proton linewidth, relaxation and polarisation transfer studies confirm the conclusion in the previous report on d(m5C-G-C-G-m5C-G) (Tran-Dinh et al Biochemistry 1984 in the press) that Z exchanges only with B whereas the latter also exchanges with S,Z in equilibrium B in equilibrium S. The present data show that even at high salt concentration where only the Z form of d(C-G-m5C-G-C-G) is observed the Z-S transition also passes through the B form as an intermediate stage. The B-Z transition takes place when the Watson-Crick hydrogen bonds are firmly maintained and is greatly favoured when there are three hydrogen bonds between the base-pairs.

Thermodynamics of the B to Z transition in poly(m5dG-dC).

“…Roy and Miles (8), however, reported a thermally driven interconversion of poly(m5dG-dC) from the B to the Z form in dilute Na+/Mg2+ solutions. Temperature-dependent conformational transitions to the Z form in poly(dG-dC) and poly(m5dG-dC) under a variety of solution conditions were subsequently reported (9)(10)(11)(12)(13)(14).…”

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.…”

“…B-form proton signals were easily assigned by comparison with spectra at the same temperatures in 0.1 M NaCl solution. The presence of the Z form was evidenced on the basis of criteria mentioned in our previous papers on d(mSC-G-C-G-m5C-G) [5] and d(C-Gm5C-G-C-G) [6] : (a) Z-form internal methyl groups of dm5C or dT residues resonate around 1.1 ppm, about 0.5 ppm upfield from the corresponding B-form signals; (b) strong negative NOE are observed on dG H8 protons of the Z form upon irradiation of the H1' protons of the same residues, showing the syn orientation of the guanine bases in the Z form. In the case of d(C-G-C-A-m5C-G-T-G-m5C-G), above 45°C the signal of the H8 proton of the dA residue in the Z form was well resolved and located about 0.06 ppm upfield from the corresponding signal of the B form.…”

“…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. For that purpose, we synthesized two decamers, d(m5C-G-C-A-m5C-G-T-G-C-G) [ [6] and d(C-A-C-G-T-G) [8].…”

Geometry of the antitumor drug ditercalinium bisintercalated into d(CpGpCpG)2 by 1H NMR.

“…This method also provides information regarding motions in DNA (17), proton exchange (18), kinetics of transition between DNA forms (19), and complex dynamics (12). Because DNA intercalators generally bind more tightly to pyrimidine-purine sequences (20) (7), which then was assumed to faithfully mimic DNA.…”