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

Abstract

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.

Raman Study of the Interaction between Polyamines and a GC Oligonucleotide

“…Thus, the difference spectra from both H 2 O and D 2 O solutions show negative fea- 7 ] is no longer exclusively in the B-form, but significant concentrations of Z-form are present (37,38). This assert is also supported by the fact that up to 40% of Z-DNA does not appreciably modify the characteristical B-form Raman spectrum (55,59).…”

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

“…Thus, slight variations in the base-to-base geometrical arrangement, which may occur upon polynucleotide structural transition, can easily be monitored by RRS : this concerns the base stacking on one hand (from the 1100-1800 em -I region), which can be mainly monitored by Raman line Downloaded by [Rutgers University] at 17:30 04 April 2015 intensity variations (the so-called "hypochromic effects", very sensitive in RRS), and the nucleoside conformation (sugar puckering and base-sugar interactions) on the other hand (from the 600-800 em -I region). In addition, the DNA typical concentration needed for the RRS measurements is much lower than that needed for classical Raman measurements : this alleviates the risks of possible DNA concentration effects which can sometimes entangle the proper salt-induced structural transitions (13).…”

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

“…In addition, RRS features of native and synthetic DNAs in aqueous solutions, obtained with various excitation wavelengths, have been found to be very sensitive to the polymer structures : like other optical spectroscopies (classical Raman, IR. CD, etc ... ), RRS in the 220-280 nm region brings its own share of structural information, and allows monitoring of changes in the helical structure as a function of DNA solvation and/or interaction in which DNA is involved (3,4).…”

“…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.…”