IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations.

Tridecamers containing a central no-base residue (X) have been synthesized and hybridized to their complementary strands, so as to constitute duplexes consisting of two hexamers separated by central mismatched X-A or X-T pairs. The effect of the introduction of this deoxyribose derivative on duplex stability was investigated by measuring UV absorbance as a function of salt concentration and temperature. As expected, the duplexes containing the abnormal base pairs (X-T and X-A) are less stable when compared to the totally complementary duplexes (A-T and T-A). The X-T mismatched duplex shows the most unstable thermodynamical behaviour. The conformational changes of these duplexes were studied by IR spectroscopy in condensed phase as a function of water content. At high relative humidity, the IR spectra show that these tridecamers form B-type double stranded duplex structures. If the water content is decreased, only the duplexes m5CGm5CGCTXAGCTTC GCGCGAATCGAAG and, to a lesser degree, m5CGm5CGCTXAGCTTC GCGGCATTCGAAG undergo a partial B---Z transition involving the methylated hexamer, the conformation of the second segment remaining of the B type. These results show that only one apurinic residue leads to a flexible junction between B and Z forms in a short duplex containing 5-methyl-2'-deoxycytidines.

Z form of poly d(A-T).poly d(A-T) in solution studied by CD and UV spectroscopies.

Near UV CD spectra, UV absorption spectra and their first derivatives have been recorded on poly d(A-T).poly d(A-T) solutions in presence of high NaCl concentration and various amounts of NiCl2. Comparison of the results presented here with those obtained for poly d(G-C).poly d(G-C) and poly d(A-C).poly d(G-T) in comparable conditions, and the I.R. and Raman data on poly d(A-T).poly d(A-T), allows us to assign the new spectra to the Z conformation of poly d(A-T).poly d(A-T) in solution. The mechanism by which nickel ions induce the B----Z interconversion in the presence of high NaCl concentration is discussed.

Interaction of transition metal ions with Z form poly d(A-C).poly d(G-T) and poly d(A-T) studied by I.R. spectroscopy.

Interactions between Ni2+, Co2+ and purine bases have been studied by I.R. spectroscopy in the case of double stranded regularly alternating purine-pyrimidine polynucleotides poly d(A-T), poly d(A-C).poly d(G-T) and poly d(G-C). The spectra of polynucleotide films have been recorded in hydration and salt content conditions which correspond to the obtention of the classical right-handed (A,B) and left-handed (Z) helical conformations. Selective deuteration of the 8C site of purines has been obtained and is used to detect interactions between the transition metal ions and the adenine or guanine bases. The spectral region between 1500 and 1250 cm-1 corresponding to base in-plane vibrations and involving also the glycosidic linkage torsion is discussed in detail. The selective interaction between the transition metal ion and the 7N site of the purine base is considered to be partly responsible for the stabilization of the base in a syn conformation, which favours the adoption by the polynucleotide (poly d(G-C), poly d(A-C).poly d(G-T) or poly d(A-T)) of a Z type conformation.

Interaction of Z form poly(dG-dC).poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy.

The secondary structures of poly(dG-dC).poly(dG-dC) in the presence of alcaline , alcaline earth and first row transition metal ions (Na+, Mg2+, Co2+, Ni2+) are investigated by infrared spectroscopy. The conformational transitions are studied as a function of the hydration of the polynucleotide and counter-ion nature and content. The use of selectively deuterated poly(dG-dC).poly(dG-dC) on the 8-carbon of guanines allows to show that a direct interaction occurs between the N7 site of guanines and the transition metal ions Co2+ and Ni2+. In the case of Mg2+, for high ion/nucleotide ratios, the interaction occurs essentially at the level of the phosphate groups. This interaction leads to a modification of the left-handed conformation. Based on the IR spectroscopy results, an explanation is proposed for the different efficiencies of these various ions to induce the B----Z transition.

Z-form induction in DNA by carcinogenic nickel compounds: an optical spectroscopy study.

The B----Z conformational transition of double-stranded poly(dG-dC) induced by various nickel salts (chloride, sulfate, subsulfide, carbonate) has been studied by ultraviolet absorption and circular dichroism. The spectra of the nickel compounds, both free and complexed with DNA, have been obtained in the visible and near infrared regions. In all cases the nickel adopts the hexacoordinated ionic form [Ni(H2O6]2+ and induces the B----Z transition of the nucleic acid at submillimolar concentrations (typically 0.4 mM). The addition to the poly(dG-dC)-poly(dG-dC) of an antitumoral drug, pentaziridinocyclodiphosphathiazene (SOAz), inhibits the B----Z transition even at a ten-fold higher nickel concentration (4 mM). Possible implications for carcinogenesis are discussed.

Spectroscopic studies of conformational transitions in double stranded DNAs in the presence of carcinogenic nickel compounds and an antitumoral drug (SOAZ).

The influence of an antitumoral drug, the pentaziridinocyclodiphosphatiazene (SOAZ), on the right----left-handed helix conformational transition of Poly (dG-dC). Poly (dG-dC) induced by carcinogenic or mutagenic Nickel compounds has been studied by ultraviolet absorbance and circular dichroïsm measurements. The B----Z transition of the polynucleotide is induced in two steps, in a similar way whatever the origin of the Nickel ions (NiCl2, NiSO4, Ni3S2, NiCO3). The midpoint of the second step (right----left-transition) is located around 0.4 mM Ni2+. The addition of SOAZ to the Poly (dG-dC). Poly (dG-dC) modifies this transition which is shifted to 2 mM Ni2+ for a 1 SOAZ/10 DNA phosphates ratio. The right-handed helix is stabilized and for a 1.5 SOAZ/phosphate ratio no B----Z transition is observed even for a tenfold amount of added Nickel (4 mM Ni2+). The addition of SOAZ to the DNA initially converted to a Z conformation by the presence of Nickel inhibits the return to the B form.