The effect of HCl on the solution structure of calf thymus DNA: A comparative study of DNA denaturation by proton and metal cations using fourier transform IR difference spectroscopy

Abstract

The interaction of HCl with calf thymus DNA was investigated in aqueous solution at pH 7-2 with H+/DNA(P) (P:phosphate) molar ratios (r) of 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform (FTIR) difference spectroscopy. Correlations between spectral changes, proton binding mode, DNA denaturation, and conformational variations are established. A comparison was also made between the ir spectra of denaturated DNA, in the presence of proton and Cu ions with similar cation concentrations. The FTIR difference spectroscopic results have shown that at low proton concentrations of r = 1/80 and 1/40 (pH 7-5), no major spectral changes occur for DNA, and the presence of H+ results in an increased base-stacking interaction and helical stability. At higher proton concentrations of r > 1/40, the proton binding to the cytosine and adenine bases begins with major destabilization of the helical duplex. As base protonation progresses, a B to C conformational conversion occurs with major DNA spectral changes. Protonation of guanine bases occurs at a high cation concentration r > 1/2 (pH < 3) with a major increase in the intensity of several DNA in-plane vibrations. Copper ion complexation with DNA exhibits marked similarities with proton at high cation concentrations (r > 1/10), whereas at low metal ion concentrations, copper-PO2 and copper-guanine N-7 bindings are predominant. No major DNA conformational transition was observed on copper ion complexation.

Aspirin‐DNA interaction studied by FTIR and laser Raman difference spectroscopy

“…The helix perturbation induced by aspirin is more pronounced than those associated with the ascorbate anion at high drug concentration [10]. However, by comparing the spectral alterations of the calf-thymus DNA in the presence of H + and Cu cations (fully melted) and aspirin (partially destabilized), the observed intensity increases of certain DNA inplane vibrations (marker bands) are larger (fourfold) for proton and copper cations, than those of the aspirin-DNA complexes (twofold) [21,22]. It is worth mentioning, that the reason for the structural dependency of aspirin-DNA complexes on drug concentration is mainly related to different types of drug-DNA complexes, formed (with different DNA binding sites) as aspirin concentration is increased.…”

An FTIR Spectroscopic Study of Calf-thymus DNA Complexation with Al(III) and Ga(III) Cations

“…Similarly, the thermal denaturation of DNA duplex causes major intensity increase for several DNA vibrational frequencies (36). The IR spectra of denatured calf-thymus DNA by acid fixation or copper coordination exhibit major intensity increase (fourfold) for certain DNA in-plane vibrations (37,38). The helix opening produces several new metal binding sites such as guanine and thymine C=O groups, adenine N-1 and cytosine N-3 atoms.…”

Specific Applications of Vibrational Spectroscopy in Biomedical Engineering

“…It is possible to study DNA samples in a solution, dehydrated fibre, film or crystalline form (Prescott et al, 1984;Taillandier et al, 1989;Taillandier & Liquier, 1992). Different factors, such as temperature, pH (Tajmir-Riahi et al, 1995), varying hydration (Falk et al, 1963;Lee et al, 2004;Pevsner & Diem, 2003;Tao et al, 1989) and ionic strength (Keller & Hartman, 1986;Taillandier et al, 1989, Taillandier & Liquier, 1992, affect the physical state of DNA samples.…”

“…IR also allows single-stranded, double-stranded and triple-stranded chains of DNA to be distinguished (Banyay et al, 2003;Taillandier & Liquier, 1992). In the literature there are plenty of data on the conformational changes induced by pH or temperature changes (Lee et al, 2004;Tajmir-Riahi et al, 1995), dehydration (Falk et al, 1963;Lee et al, 2004) (Hackl et al, 2005;Matsui et al, 2009). IR spectroscopy is also a powerful technique in investigating the interaction of DNA with drugs (Taillandier & Liquier, 1992).…”