The B–Z transition in two synthetic oligonucleotides: d(C-2-amino-ACGTG) and d(m⁵CGCAm⁵CGTGCG) studied by IR, NMR and CD spectroscopies

Abstract

The sequences CA'CGTG (where A' = 2-aminodeoxyadenosine) and m5CGCAm5CGTGCG are prepared and studied by IR, CD and 1H-NMR. Infrared spectra demonstrate the capacity of the modified hexamer and decamer to adopt a Z conformation. The influence of the NH2 substitution on the adenine or of the methylated terminal part of the decamer acting with the increase of the DNA concentration stabilizes the Z conformation at room temperature in low humidity films. Very weak proportion of Z conformation is detected in UV dilute solutions. In more concentrated NMR solutions, the Z proportion induced by high salt content is only 20-25%. The effects of the concentration and of the covalent modification of the bases are discussed.

Z Helix-coil Transition of d(C-Br8G-C-G-C-Br8G) Studied by CD,1H-NMR and IR Spectroscopies

“…Therefore, in condensed phases, the Z ~coil equilibrium is totally displaced towards the first configuration of d(C-Br"G-C-G-C-Br"G) even at 70°C. Similar effect of the concentration has been previously reported in the case of d(C-2amino A-C-G-T-G) and d(m 5 C-G-C-A-m 5 C-G-T-G-C-G) studied by CD, 1 H-NMR and IR spectroscopic technics (13) which shows that the concentration effect should be important in stabilizing the Z form in biological systems.…”

“…Recent reports have shown that IR, 1 H-NMR and CD analysis, under various experimental conditions (temperatures, DNA's and ionic concentrations, solvent) of oligonucleotides d(C-Gh containing 5-methyl cytosine residues in different positions (10,12), d(C-2amino A-C-G-T-G) and d(m 5 C-G-C-A-m 5 C-G-T-G-C-G) (13) were effective techniques to study B and Z double helix conformations. In the case of methylated hexamer, the formation of the Z double helix which is dependent on salt concentration was found by 1 H-NMR to take place via formation of a B double helix even in high salt solution (4 M NaCl) (10,11).…”

“…In the case of methylated hexamer, the formation of the Z double helix which is dependent on salt concentration was found by 1 H-NMR to take place via formation of a B double helix even in high salt solution (4 M NaCl) (10,11). On the other hand, the IR spectroscopy on condensed phase has shown the existence of Z form for poly(dA-dC)• poly(dG-dT) (14) as well as for d(C-2amino A-C-G-T-G) and d(m 5 C-G-C-A-m 5 C-G-T-G-C-G) whereas in solution only a fraction of the two latter ones undergoes the B-Z transition (13).…”

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

“…After zerofilling in the tl dimension, a 1024 x 1024 data point matrix was obtained and then Fourier-transformed in both dimensions. Spectra were line-broadened by a sine bell weighing in both d [15]. In the case of d(C-2aminoA-C-G-T-G) proton assignment was carried out mainly by comparison with d(C-A-C-G-T-G) [8] and by selective protonproton decoupling when necessary.…”

Modified oligonucleotides as alternatives to the synthesis of mixed probes for the screening of cDNA libraries.

“…All oligonucleotides were manually synthesized by the solid-phase phosphotriester method (12) using triisopropylsulfonylnitrotriazole as coupling agent (13) on a 2-mmol scale. The modified nucleoside phosphotriesters t4T, t6G, and n2A have been described (14)(15)(16).…”