Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions

Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2'F-araC and 2'F-riboG, induce the formation of the Z-form under low ionic strength. We show that oligomers entirely made of these two nucleosides exclusively produce left-handed duplexes that bind to the Zα domain of ADAR1. The effect of the two nucleotides is so dramatic that Z-form duplexes are the only species observed in 10 mM sodium phosphate buffer and neutral pH, and no B-form is observed at any temperature. Hence, in contrast to other studies reporting formation of Z/B-form equilibria by a preference for purine glycosidic angles in syn, our NMR and computational work revealed that sequential 2'F…H2N and intramolecular 3'H…N3' interactions stabilize the left-handed helix. The equilibrium between B- and Z- forms is slow in the 19F NMR time scale (≥ms), and each conformation exhibited unprecedented chemical shift differences in the 19F signals. This observation led to a reliable estimation of the relative population of B and Z species and enabled us to monitor B-Z transitions under different conditions. The unique features of 2'F-modified DNA should thus be a valuable addition to existing techniques for specific detection of new Z-binding proteins and ligands.

Chiroptical Properties of Z-DNA Using Ionic Porphyrins and Metalloporphyrins

The non-covalent interaction of achiral porphyrins with nucleic acids has been extensively studied, and various macrocycles have been indeed utilized as reporters of different sequences of DNA bases. Nevertheless, few studies have been published on the capability of these macrocycles to discriminate among the various nucleic acid conformations. Circular dichroism spectroscopy allowed to characterize the binding of several cationic and anionic mesoporphyrins and metallo derivatives with Z-DNA, in order to exploit the functionality of these systems as probes, storing system, and logic gate.

Effect of Different Z-Inducers on the Stabilization of Z Portion in BZ-DNA Sequence: Correlation Between Experimental and Simulation Data

In this study we show the outstanding agreement between simulation and experimental data concerning the efficient stabilization effect by NaCl of Z conformation. We demonstrate by circular dichroism (CD) experiments that Na(+) not only is able to induce a B to Z form transition in a short (GC)3 alternated portion of a sequence having 17 basis, but also is the best stabilizer in comparison with other Z inducers used (spermine and NiCl2). This result was confirmed by free energy calculations.

Circular dichroism study of supramolecular assemblies of guanosine 5'-monophosphate

Concentration and temperature dependent studies of the circular dichroism of dianionic guanosine 5'-monophosphate (5'-GMP), where the cation was Na(+), K(+), or Rb(+) ion, were done to obtain information regarding the nature of the self-assembled 5'-GMP species in aqueous solution, including G-quartets and other structures. Concentrations in the 0.05-0.85 M range and temperatures in the 5-50 °C range were used. At the highest concentrations and 5 °C, Na(2)(5'-GMP) and K(2)(5'-GMP) formed a cholesteric phase, but Rb(2)(5'-GMP) did not. Evidence for antiparallel base stacking (stacked with opposite polarity; head to head) was observed for Rb(2)(5'-GMP) but not for the Na(+) or K(+) salts. This structure, believed to be G-quartets, had a melting temperature of 15 °C and dissociated into a second associated species as the temperature increased. The latter was present to the greatest extent at ∼40 °C, and it is characterized by a prominent negative CD band at 306 nm, which may be indicative of an X-DNA type of structure (an expanded G-quartet) or base-stacked monomers or dimers. The same negative band appeared at 310 nm in the CD spectra of K(2)(5'-GMP) and Na(2)(5'-GMP) but was much less intense in the latter case. K(2)(5'-GMP) also formed a noncholesteric phase containing at least two different species, one more stable at low temperatures and the other more stable at higher temperatures, similar to Rb(2)(5'-GMP). (1)H NMR spectroscopy was used to assist in the interpretation of the CD spectra.