DNA structure studies by resonance Raman spectroscopy

Poly( dl-dC) in aqueous solution can undergo different equilibrium geometries, which strongly depend on salt nature and concentrations. These equilibrium structures have been monitored by resonance Raman spectroscopy (RRS) measurements in the ultraviolet region, i. e. by using 257 and 281 nm laser excitation wavelengths which favor the resonance enhancement of the Raman contributions from inosine and cytosine residues of poly( dl-dC), respectively. Spectral changes depending on the NaCI concentration and on the presence orNe+ ions have been observed and interpreted in comparison with RRS results previously obtained for other alternating purine-pyrimidine polydeoxyribonucleotides, i.e. poly(dG-dC), poly(d.Adn and poly(d.A-dC).poly(dG-dT), which also showed B to Z conformational transitions in varying the salt concentrations. It is shown here that : i) the base stacking geometries are nearly the same in the high-salt form (5 M NaCl) of poly( dl-dC) as in the low-salt form (0.1 M NaCI) ofthe polymer, ii) however, the high-salt structure yields important differences from a B-helix (obtained in low-salt solution) as regards the nucleoside conformations (sugar puckering and base-sugar orientation), and: iii) the addition of9 mM NiC1 2 in the high-salt(5 M NaCI) solution ofpoly(dl-dC) induces the Z-conformation of the polymer.

Section: Downloaded By [Rutgers University] At 17:30 04 April 2015mentioning

confidence: 98%

Conformational Transitions of Poly(dl-dC) in Aqueous Solution as Studied by Ultraviolet Resonance Raman Spectroscopy

Miškovský¹,

Tomkova²,

Chinsky³

et al. 1993

“…As far as UV RRS is concerned for investigating structural changes which may occurin oligo-and polynucleotide duplexes, as a function of the polymer solvation, we have recently studied the B -Z transitions in ( dG-d5mC) 3 (7), poly( dG-dC) (8,9), poly(dA-dT) (9, 3) and even natural DNA from Chicken Erythrocytes (4). In this last case, marker bands of a left form were observed under specific conditions, i.e.…”

Section: Introductionmentioning

confidence: 99%

Ultraviolet Resonance Raman Marker Bands of the Right to Left Helix Structure Transitions in DNA and Polynucleotide Model Compounds

Miškovský¹,

Laigle²,

Chinsky³

et al. 1992

The right to left helix structural transition in purine-pyrimidine alternating copolymers has been extensively studied by vibrational spectroscopies, amongst many other experimental approaches. Here, the use of resonance Raman spectroscopy in the ultraviolet region (223-, 257- and 281 nm excitation wavelengths) to monitor such structural changes is reviewed in the light of new results obtained on poly(dA-dC).poly(dG-dT) on one hand, and the previous results obtained on poly(dG-dC)2, poly(dA-dT)2 and natural DNA (Chicken erythrocytes) on the other. It is now possible to define B----Z transition marker bands involving the proper bases, which show a similar behaviour on structural transition whatever the composition of alternating purine-pyrimidine sequences: the 1580- and 1487 cm-1 lines of the purines, the 1486- and 1294 cm-1 lines of the pyrimidines are good markers in the vibrational spectra recorded at various UV excitation wavelengths.

“…Such an enhancement of a Raman line at 1642 em -I has also been observed in the poly( dG-dC).poly( dG-dC)-mitomycin C complexes (33) with a 257 nm excitation wavelength. This band is the only visible contribution of cytosine in the spectra of poly( dG-dC).poly( dG-dC) (39,41 ). It has been attributed to 2C=O stretching motion of cytosine (47).…”

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

confidence: 92%

“…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%

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

Berthelier¹,

Laigle²,

Jollès³

et al. 1995

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.