Detection of the sites of alkylation in DNA and polynucleotides by laser Raman spectroscopy

Interaction of Et2SnCl2 with 5'-IMP and 5'-GMP

The interactions of Et2SnCl2 with 5'-IMP and 5'-GMP have been studied in aqueous solutions by 1H- and 31P-NMR spectroscopy as a function of pH. At low pH values (< 4.0) Sn(IV) interacts with the pyrophosphate oxygens of these nucleotides. At intermediate pH values (4-9.5) no interaction of the metal with the nucleotides take place, while at pH > 9.5 the sugar O'2 and O'3 atoms are the preferred coordination sites. In addition, the solid adducts obtained from aqueous solutions at pH = 3-4 of the above interactions correspond to formulae; (Et2Sn)2(5'-IMP)2(H2O) and (Et2Sn)3(5'-GMP)2(OH)2(H2O)2 as their elemental analysis show. IR spectra and solid state 13C, 31P-NMR spectra 119Sn Mössbauer and solution 119Sn-NMR spectra once more confirm the pyrophosphate involvement in bonding with Sn(IV) in oligomeric or polymeric structures and trigonal bipyramidal or octahedral geometries.

Comparative study of the interactions of cisplatin and carboplatin with nucleotides using UV resonance Raman spectroscopy

We have obtained the UV excited resonance Raman spectra of five mononucleotides bound to cisplatin and to carboplatin using excitation in resonance with the first electronic absorption bands of the nucleotide bases. Substantial changes in the spectra are observed following interaction with both platinum drugs, indicating modifications to nucleotide structure. Pt (II) binds to base portions of the nucleotide molecules, altering their normal modes of vibration significantly. We present comparative data of cisplatin and carboplatin, and discuss the implications of these results. The kinetics of the drug/nucleotide reactions differ, but final products are found to be similar.

Far-infrared study of the vibrational modes of 5'-GMP gels and crystals of Na+ and K+

Five Far-Infrared (50-600 cm-1) spectra are presented: the sodium and potassium salts of 5' Guanosine Monophosphate (GMP), each salt in both the gel and crystal conformations, and poly(rG). Measurements were performed at a sample temperature of 10 K under vacuum with a liquid He-cooled bolometer. The spectra were fit with Lorentzians and assignments are suggested. There are noteworthy differences in oscillator strengths and frequencies of the bands between all spectra. We report the tentative observation of a 100 cm-1 mode which is in the neighborhood of a mode observed by Raman spectroscopy in solution (1) and dried gels (2).

Raman spectroscopic study of the effects of Ca2+, Mg2+, Zn2+, and Cd2+ ions on calf thymus DNA: binding sites and conformational changes

The interaction of Mg2+, Ca2+, Zn2+, and Cd2+ with calf thymus DNA has been investigated by Raman spectroscopy. These spectra reveal that all of these ions, and particularly Zn2+, bind to phosphate groups of DNA, causing a slight structural change in the polynucleotide at very small metal: DNA (P) concentration ratio (ca. 1:30). This results in increased base-stacking interactions, with negligible change of the B conformation of DNA. Contrary to Zn2+ and Cd2+, which interact extensively with the nucleic bases (particularly at the N7 position of guanine), the alkaline-earth metal ions are bound almost exclusively to the phosphate groups. The affinity of both the Zn2+ and Cd2+ ions for G.C base pairs is comparable, but the Cd2+ ions interact more extensively with A.T pairs than Zn2+ ions. Interstrand cross-linking through the N3 atom of cytosine is suggested in the presence of Zn2+, but not Cd2+.

A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes

The interaction of calf-thymus DNA with Cu(II) and Pb(II) ions has been investigated in H2O and D2O solutions at physiological pH, using laser Raman spectroscopy. The results confirm the destabilizing effect of Cu2+ ions, which are shown to bind strongly to the guanine and cytidine bases, perturbing the A-T base pairs and disrupting the double-helical structure of DNA, whose conformation is markedly altered by these interactions. Earlier claims that Pb2+ ions destabilize DNA are not supported by the present study. These ions are found to interact only weakly with the nucleic bases, binding to the N7 position of the guanine bases and also interacting with the A-T pairs. Both types of ions are found to interact with the charged phosphate groups of DNA, although these sites are preferred over the nucleic bases by Pb2+ ions.

Interaction of adriamycin with DNA as studied by resonance Raman spectroscopy

Raman and resonance Raman spectra of the complex DNA-adriamycin in aqueous solution have been recorded and analysed. Calf thymus DNA was used and it is found that in the complex DNA-adriamycin the chromophore of adriamycin is intercalated in the GC sequences. The substituents on the rings give hydrogen bonding interactions with the base pairs above and below the intercalation site. It is suggested from the Raman and resonance Raman spectral modifications that the phenolic groups of the chromophore are involved in the drug-DNA intercalation, in addition to pi-pi, hydroxyl and amino group interactions.

Physical association modeling of DNA alkylation. Some DNA conformational aspects

The widespread occurrence of physical binding between biological macromolecules and small molecules has prompted us to hypothesize that physical binding contributes to DNA alkylation specificity. The preferred physical binding sites for a CH+3-like test probe were predicted for several sequences of DNA using molecular mechanics free space calculation methods. Sequences containing A = T basepairs direct physical binding to the minor groove, whereas sequences containing G identical to C basepairs direct physical binding to the major groove. Physical binding calculations were also performed for model 'unwound' DNA conformations. The results of the test probe studies were subsequently employed as starting points to predict the preferred physical binding sites for the more complicated case of an actual alkylating agent, the dimethylaziridinium ion. These studies demonstrate that physical binding specificity is highly dependent upon DNA sequence and conformation, and correlates well with the DNA alkylation site specificity observed for alkylating agents in th dimethylaziridine class.

Circular dichroism anisotrophy of DNA with different modifications at N7 of guanine

The complexex DNA-Ag1+, DNA-Cu1+, protonated DNA and DNA methylated at N7 of guanine were oriented by pumping the solutions through a multicapillary cell in the direction of a light beam. The CD components along the DNA axis, delta epsilon parallel, and normal to it, 2 delta epsilon perpendicular, were calculated from the CD spectra of the oriented samples by the method of Chung and Holzwarth, (1975) J. Mol. Biol. 92, 449--466. It was shown that in most cases, except that of the protonated DNA, the degree of orientation was only slightly less than that for pure DNA. This demonstrated the absence of aggregation and of appreciable denaturation. In all cases the modifications of DNA give rise to a negative component 2 delta epsilon perpendicular, whose magnitude increased as the extent of modification increased. From both the CD spectra of non-oriented samples and the absorption spectra, an inference is drawn that Ag1+ and Cu1+ are attached to the same site as CH3 groups i.e., to the N7 atom of guanine. Proton transfer along the H-bond from the N1 atom of G to the N3 atom of the complementary cytosine is suggested to be a result of the modifications, although the case of H+-DNA may differ from the others. Based on the CD spectra for the anisotropic components, delta epsilon parallel and 2 delta epsilon perpendicular, it is proposed that ligand binding is accompanied by winding of the DNA helix.

Ultraviolet resonance Raman study of DNA and of its interaction with actinomycin D

The DNA-Actinomycin D interaction has been studied by resonance Raman effect using DNA as chromophore. First, the resonance Raman spectra of DNA obtained with a U.V. excitation at wavelengths of 300 nm and 280 nm are presented. The main Raman hands are assigned to the convenient nucleic bases by comparison with the spectra of mononucleotides obtained under the same experimental conditions. In particular, with a 300 nm excitation, the 1582 cm-1 line is provided by adenine, while the 1492 cm-1 one is almost exclusively due to guanine. Then, the DNA-Actinomycin D complex has been studied: the line enhancements and the specificity of the resonance permits the displaying of the DNA spectrum free of any contribution of Actinomycin. The interaction provides a large intensity decrease of the 1492 cm-1 guanine line: this is a direct consequence of the orbital overlapping of the guanine 2-aminogroup with the ring nitrogen of Actinomycin in the DNA-Actinomycin pi complex.

Form of DNA and the nature of interactions with proteins in chromatin

Studies of native chromatins and of isolated nucleosomes (from calf thymus) show that the DNA is in the B form or modified B form. This was determined by Raman spectroscopy of chromatins, of nucleosomes (from calf thymus) and of DNA fibres and directly correlated with X-ray diffraction studies. The Raman spectra of three forms of DNA (A, B and C) have been characterized in fibres both by X-ray diffraction and Raman spectroscopy on the same sample. In particular, the Raman spectrum of the C form of DNA is characterized by a band of about 870 cm(-1). For the first time, chromatins of different origins with increasing content of non-histone proteins have been investigated by Raman spectroscopy. The site of interaction of the non-histone proteins appears to involve the N7 position of guanine while the histone core does not interact at this site. It is proposed that the mechanism of specific recognition in chromatin involves the large groove.