Poly[d(A-T)-Cs+] conformations studied by IR spectroscopy.
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Nucleic Acid Conformation↗
Biomedical subjects
J A Taboury
Publications and source records attributed to J A Taboury.
[Cystine calculi. In vitro solubility and chemical structure].
A series of cystine stones extracted from the same subject by pyelotomy was used to study the in vitro solubility of these stones in various solutions. Isotonic bicarbonated saline presented a definite dissolving action, but the stone dissolved relatively slowly alpha-mercapto-propionyl-glycine was much more active, even when mixed urine. N-acetylcystine had the same degree of effectiveness as alpha-mercapto-propionyl-glycine. One stone in this series, which was partially covered by a coating of calcium phosphate, dissolved much more slowly than the other stones. In subjects with cystine stones, longstanding large stones are frequently mixtures of phosphates and cystine and, in 21 cases, chemical analyses and infra-red spectrography demonstrated the presence of calcium phosphate on the surface or in the inferior of these stones, associated with ammoniaco-magnesium phosphate in three cases. The presence of phosphates makes oral medical treatment ineffective, but mixed stones are more friable than pure cystine stones and are therefore easier to treat by extracorporeal lithotripsy.
Chemical Phenomena↗
Right- and left-handed helixes of poly[d(A-T)].poly[d(A-T)] investigated by infrared spectroscopy.
The secondary structures of double-stranded poly[d(A-T)].poly[d(A-T)] in films have been studied by IR spectroscopy with three different counterions (Na+, Cs+, and Ni2+) and a wide variety of water content conditions (relative humidity between 100 and 47%). In addition to the A-, B-, C-, and D-form spectra, a new IR spectrum has been obtained in the presence of nickel ions. The IR spectra of Ni2+-poly[d(A-T)].poly[d(A-T)] films are analyzed by comparison with previously assigned IR spectra of left-handed poly[d(G-C)].poly[d(G-C)] and poly[d(A-C)].poly[d(G-T)], and it is possible to conclude that they reflect a Z-type structure for poly[d(A-T)].poly[d(A-T)]. The Z conformation has been favored by the high polynucleotide concentration, by the low water content of the films, and by specific interactions of the transition metal ions with the purine bases stabilized in a syn conformation. A structuration of the water hydration molecules around the double-stranded Ni2+-poly[d(A-T)].poly[d(A-T)] is shown by the presence of a strong sharp water band at 1615 cm-1.
Nucleic Acid Conformation↗
Infrared spectral studies of the non regularly alternating purine-pyrimidine hexamers d(m5CGGCM5CG), d(CBr8GGCCBr8G) and d(CGCGGC).
The oligonucleotides d(m5CGGCm5CG), d(CBr8GGCCBr8G) and d(CGCGGC) have been prepared and studied by infrared spectroscopy. The three sequences contain two GC pairs which are out of purine-pyrimidine alternation with the rest of the sequence. From the IR data of the d(m5CGGCm5CG) hexamer, it is shown that all of the dG residues adopt a syn conformation. The marker IR bands for the C3' endo syn conformation are at 1410, 1354, 1320 and 925 cm-1 whereas those for the C2' endo anti conformation at 1420, 1374 and 890 cm-1 are clearly absent. This result implies that the two adjacent guanines of the d(m5CGGCm5CG) sequence are in syn conformation. It is suggested that duplex formation occurs in d(CGCGGC) films and that all of the guanines are in syn conformation. In contrast, the central non-brominated guanine of the d(CBr8GGCCBr8G) hexamer is found in anti conformation, as expected in a Z type structure of the non-alternating region.
Base Sequence↗
Right-handed and left-handed helices of poly(dA-dC) X (dG-dT).
The secondary structures of poly(dA-dC) X (dG-dT) were studied using CD and IR spectroscopies. We give spectroscopic evidence of secondary structure transitions of poly(dA-dC) X (dG-dT) from a B to a Z-like helix, induced by transition metal ions (Ni2+) in presence of high concentrations of Cs+ and Na+. In the presence of Na+, the B in equilibrium Z transition occurs at any temperature, whereas premelting conditions are required in presence of Cs+. For these two alkali ions the Z-like form is only induced by Ni2+ ions through their specific interactions at N7 of purines, under conditions of low water activity due to the high alkali salt concentration. We also show that the CD spectrum obtained in presence of Cs+ ions and characterized by a negative band at 275 nm, cannot be interpreted in terms of Z-like left-handed helix but reflects a modified B right-handed helix.
Circular Dichroism↗
Z helix-coil transition of d(C-Br8G-C-G-C-Br8G) studied by CD, 1H-NMR and IR spectroscopies.
The conformation of d(C-Br8G-C-G-C-Br8G) in aqueous solution was studied by CD and 1H-NMR spectroscopy and in condensed phase by IR spectroscopy. Whether in 0.1 M or 3 M NaCl solution or in film the only double helical structure adopted by brominated d(C-G)3 oligomer is the Z form. The IR spectrum of the film presents all the characteristic absorptions of the Z conformation and in particular is indicative of a syn conformation for the central guanosine as well as for the brominated one. Imino proton resonances of d(C-Br8G-C-G-C-Br8G) demonstrating the duplex formation were observed up to 60 degrees C. It is interesting to note that the significant highfield shifts of the dC H5" exocyclic sugar protons characteristic of the non exchangeable proton spectra of d(C-G)3 containing 5-methyl dC residues in the Z form were also detected in the proton spectrum of brominated oligomer. Whereas formation of the Z helix of methylated d(C-G)3 oligomers dependent on the salt concentration was found to occur via the preliminary formation of a B helix even in 4 M NaCl solution, the Z helix of d(C-Br8G-C-G-C-Br8G) is obtained directly from the coil form. However, IR data suggest that in the Z form of d(C-Br8G-C-G-C-Br8G), the overlapping of the base planes should be slightly different in comparison with the stacking observed in d(C-G)3 crystals. The kinetic data (activation energy and lifetime) of the Z helix-coil transition of brominated d(C-G)3 are compared to those of the B helix-coil transition observed for methylated d(C-G)3 in 0.1 M NaCl solution while the thermodynamic data of these two reactions (enthalpy and midpoint temperature) are slightly different.
Base Sequence↗
[Calcium oxalate monohydrate (whewellite) renal lithiasis].
Pure calcium oxalate monohydrate lithiasis is rare--about 5 to 10% of total renal lithiases. The proportion is the same in men and women. Pure calcium oxalate stones are a polished dark brown color, and are very hard. They are visualized radiologically as regular and homogeneous. From a biological standpoint, this type of stone is frequently associated with normal calciuria and oxaluria. Pure calcium oxalate monohydrate stones rarely evolve.
Adult↗
Left-handed helical structure of poly[d(A-C)].poly[d(G-T)] studied by infrared spectroscopy.
Infrared spectroscopic studies demonstrate the ability of poly[d(A-C)].poly[d(G-T)] to adopt a Z-type conformation. The Z form of the unmodified polynucleotide is induced by Ni2+ counterions and not by Na+. The B----Z equilibrium is shifted at room temperature, in the presence of 1 Ni2+/nucleotide, by an increase in the concentration of poly[d(A-C)].poly[d(G-T)]. The importance of specific binding of Ni2+ ions on the N7 site of purines in the stabilization of the Z form is also discussed.
Cations↗
The B----Z transition in two synthetic oligonucleotides: d(C-2-amino-ACGTG) and d(m5CGCAm5CGTGCG) studied by IR, NMR and CD spectroscopies.
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.
5-Methylcytosine↗
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.
Cations, Divalent↗
Experimental and calculated study of the vibrational modes of poly(dG-dC).poly(dG-dC) in B and Z conformations.
Infrared spectra of the B and Z forms of poly(dG-dC).poly(dG-dC) are presented. Experimental assignments relative to certain vibration modes have been confirmed by calculation based on the GF-Wilson method. The calculated results show that only the geometry change between B and Z forms, is responsible for the observed modifications in the vibrational spectra.
Kinetics↗
[Polymorphism of the left-handed helix (Z form) of poly(dG-dC).poly(dG-dC) induced by MgCl2, studied by infrared spectroscopy].
The existence of a left-handed double-helical DNA, called Z-DNA was proved by X-ray crystallographic analysis of the hexanucleotide d(CpGpCpGpCpG). The possible biological relevance of the Z conformation is enhanced by recent studies using immunostaining. Antibodies against Z-DNA have been raised and used to detect the Z conformation in polytene and mammal chromosomes. In this work we have studied the conditions necessary to generate the transition from the right-handed to the left-handed conformation of poly d(G-C).poly d(G-C) exposed to various concentrations of MgCl2 and various relative humidities. The infrared (IR) spectra were used to characterize the different conformations. Only below 0.5 Mg2+ ion per nucleotide we have observed the right-handed helix. Above 1 Mg2+ ion per nucleotide, the left-handed helix is always present under low and high relative humidity conditions. Furthermore, under low relative humidity and high salt content conditions we found a new IR spectrum which can be correlated with a polymorphic Z form, called here Z degree form.
DNA↗
[Monohydrate and dihydrate oxalic lithiasis. Calculi, their macroscopic structure (radiographic and therapeutic impact). Calciuria and oxaluria].
Calculi of pure calcium oxalate monohydroxide are hard, polish, dark brown stones, of a very tenuous crystalline structure. On the contrary, calculi of pure bihydroxide oxalate are clear irregular stones with a spiky surface. They are more friable and less hard than monohydroxide oxalate stones. Monohydroxide oxalate stones radiologically are regular and homogeneous, whereas bihydroxide oxalate stones have an irregular aspect. Monohydroxide oxalic lithiasis is less frequent than bihydroxide oxalic lithiasis. The proportion of monohydroxide lithiasis is the same in men and women whereas bihydroxide lithiasis is more frequent in men. Of a biologic point of view, in monohydroxide lithiasis, calciuria and oxaluria are often normal while proportion of hypercalciuria and hyperoxaluria is more important in bihydroxide lithiasis. Evolutivity is clearly inferior in monohydroxide lithiasis than in bihydroxide lithiasis.
Adult↗