The poly dA strand of poly dA.poly dT adopts an A-form in solution: a UV resonance Raman study

Jollès, Béatrice; Laigle, Alain; Chinsky, L.; Turpin, Pierre‐Yves

doi:10.1093/nar/13.6.2075

Cited by 66 publications

(31 citation statements)

References 12 publications

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“…This aberrant drug binding behavior suggests that the homopolymer duplex possesses features that distinguish it from classic, B-DNA double helices. This conclusion, which is based exclusively on thermodynamic data, is consistent with the results of structural studies that suggest that the poly(dA)-poly(dT) duplex exists in an altered B conformation (29)(30)(31)(32)(33)(34)(35) that is more highly hydrated (36). These structural studies provide us with a microscopic framework in which to develop a molecular interpretation for the entropy-driven process we observe for ligand binding to the poly(dA)-poly(dT) duplex.…”

Section: Dnasupporting

confidence: 84%

See 1 more Smart Citation

Enthalpy-entropy compensations in drug-DNA binding studies.

Breslauer

Remeta

Chou

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

227

225

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We present a comparative study of calorimetrically derived thermodynamic proffles for the binding of a series of drugs with selected DNA poly[d(A-T)]-poly[d(A-T)] behaves thermody-namically as the more "normal" host duplex toward drug binding, whereas the entropy-driven binding to the poly(dA)-poly(dT) duplex represents "aberrant" behavior. Furthermore, since each of the four drugs exhibits different modes of DNA binding, we conclude that the observed entropy-driven behavior for binding to poly(dA)-poly(dT) reflects an intrinsic property of the homopolymer duplex that is perturbed in a common manner upon ligation rather than a common property of all four binding ligands. To rationalize the large positive entropy changes that drive drug complexation with the poly-(dA)-poly(dT) duplex, we propose a model that emphasizes binding-induced perturbations of the more highly hydrated, altered B conformation of the homopolymer. Our results suggest that an aberrant thermodynamic binding proffle may reflect an unusual DNA conformation in the host duplex. However, before such a conclusion can be reached, complete

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Section: Dnasupporting

confidence: 84%

“…A large number of studies suggest that poly(dA)poly(dT) exists in solution in a non-B conformation (29)(30)(31)(32)(33)(34)(35). Drug binding to this altered conformation may induce the host duplex into a B conformation.…”

Section: Dnamentioning

confidence: 99%

Enthalpy-entropy compensations in drug-DNA binding studies.

Breslauer

Remeta

Chou

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

227

225

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“…Datachrom pulsed YAG and dye laser system. Details of the Raman setup and of the acquisition system have been described previously (30)(31)(32).…”

Section: Methodsmentioning

confidence: 99%

The Concentration Dependence of the Right to Left Conformational Transition in Natural DNA Identified by Raman Spectroscopy

Miškovský

Chinsky²,

Laigle³

et al. 1989

Journal of Biomolecular Structure and Dynamics

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The classical and resonance Raman spectra of DNA from Chicken Erythrocytes have been obtained for different DNA concentrations in solution with low and high ionic strengths. The classical Raman spectra of 30 mg/ml DNA solutions were measured in varying the sodium chloride concentration from 0.1 to 4.5 M NaCl. An increase in the salt content of the solution leads to spectral changes in the 600-700 cm-1 region, indicating a C2' endo/anti to C3' endo/syn conformational transition of the purine residues. Other changes around 840 cm-1, due to the antisymmetrical stretching vibration of the PO2 group, are also detected: they were characteristic for the B----Z transition in model systems such as poly(dG-dC).poly(dG-dC). The resonance Raman spectra of low (1 mg/ml) and high (30 mg/ml) concentrated DNA solutions were obtained with low (0.1 M) and high (4.5 M) NaCl contents, in using a 284 nm excitation wavelength. No change was observed in the intensities and band positions in the low and high salt solutions of low concentrated DNA. Thus it is assumed that the DNA structure remains unchanged whatever the salt concentration for low concentrated DNA. In contrast, great modifications of the intensities and positions of some lines were found in the spectra of high DNA concentration solution when the NaCl content is increased up to 4.5 M: these changes resemble to some extent those observed in the study of B----Z transition of several polynucleotide model compounds. It is assumed that the right-handed to left-handed conformational transition may occur in certain sections of natural DNA, likely containing alternating purine-pyrimidine sequences, when the DNA concentration is sufficiently important.

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“…There are no such 5'-TG sites in the oligonucleotides chosen in the present study. The assignment of all Raman lines and the relative intensities of their constituents have been carried out using results obtained with UV excitation of mononucleotides (34)(35)(36)(37)(38), 257 nm excitation of polynucleotides containing GC base pairs (39)(40)(41), AT base pairs (38,(41)(42)(43) and A-C/G-T copolymers (43). The assignmentofthe Raman lines as well as the relative intensities of the constituent nucleotides with a 257 nm excitation wavelength are shown in Table I.…”

Section: Localization Of the Distortions By The Use Of Chemical Probesmentioning

confidence: 99%

“…The assignmentofthe Raman lines as well as the relative intensities of the constituent nucleotides with a 257 nm excitation wavelength are shown in Table I. In resonance Raman spectra, the relative contribution of the different bases is somewhat difficult to establish since the Raman intensity also depends on the structure of the nucleic acid (26,38,44). Nevertheless, taking into account the intensities of single mononucleotides (Table I) to 25% of the total intensity of the lines at 1486 em -1 and 1580 em -1 .…”

Section: Localization Of the Distortions By The Use Of Chemical Probesmentioning

confidence: 99%

Distortion After Monofunctional Alkylation by Mitomycin C of a Dodecamer Containing its Major Binding Site

Berthelier¹,

Laigle²,

Jollès³

et al. 1995

Journal of Biomolecular Structure and Dynamics

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The structural distortions of the duplex dodecamer d(ATTAACGTTAAT)2 monofunctionally alkylated by mitomycin C have been studied by the use of chemical probes reactivity and resonance Raman spectroscopy. This sequence contains the 5'-ACGT sequence for which mitomycin C was determined to present the best affinity (S. Kumar, R. Lipman, and M. Tomasz, Biochemistry 31, 1399 (1992)). Raman spectroscopy as well as osmium tetroxyde reactivity indicate that the distortion of the double helix structure is located around the central CG bases. Mitomycin C reacts exclusively with the 2-amino group of guanine and this binding does not disrupt the inter bases H-bonds, as indicated by chloroacetaldehyde reactivity. Although resonance Raman spectroscopy does not allow the handedness of the monoalkylated CG/GC sequence to be determined, it indicates a similarity between the base stacking and that which would be observed for alternating purine/pyrimidine sequences at high salt concentration.

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The poly dA strand of poly dA.poly dT adopts an A-form in solution: a UV resonance Raman study

Cited by 66 publications

References 12 publications

Enthalpy-entropy compensations in drug-DNA binding studies.

Enthalpy-entropy compensations in drug-DNA binding studies.

The Concentration Dependence of the Right to Left Conformational Transition in Natural DNA Identified by Raman Spectroscopy

Distortion After Monofunctional Alkylation by Mitomycin C of a Dodecamer Containing its Major Binding Site

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