Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Abstract

Differential scanning calorimetry, laser Raman spectroscopy, optical densitometry, and pH potentiometry have been used to investigate DNA melting profiles in the presence of the chloride salts of Ba2+, Sr2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Metal-DNA interactions have been observed for the molar ratio [M2+]/[PO2-] = 0.6 in aqueous solutions containing 5% by weight of 160 bp mononucleosomal calf thymus DNA. All of the alkaline earth metals, plus Mn2+, elevate the melting temperature of DNA (Tm > 75.5 degrees C), whereas the transition metals Co2+, Ni2+, and Cd2+ lower Tm. Calorimetric (delta Hcal) and van't Hoff (delta HVH) enthalpies of melting range from 6.2-8.7 kcal/mol bp and 75.6-188.6 kcal/mol cooperative unit, respectively, and entropies from 17.5 to 24.7 cal/K mol bp. The average number of base pairs in a cooperative melting unit (<nmelt>) varied from 11.3 to 28.1. No dichotomy was observed between alkaline earth and transition DNA-metal complexes for any of the thermodynamic parameters other than their effects on Tm. These results complement Raman difference spectra, which reveal decreases in backbone order, base unstacking, distortion of glycosyl torsion angles, and rupture of hydrogen bonds, which occur after thermal denaturation. Raman difference spectroscopy shows that transition metals interact with the N7 atom of guanine in duplex DNA. A broader range of interaction sites with single-stranded DNA includes ionic phosphates, the N1 and N7 atoms of purines, and the N3 atom of pyrimidines. For alkaline earth metals, very little interaction was observed with duplex DNA, whereas spectra of single-stranded complexes are very similar to those of melted DNA without metal. However, difference spectra reveal some metal-specific perturbations at 1092 cm-1 (nPO2-), 1258 cm-1 (dC, dA), and 1668 cm-1 (nC==O, dNH2 dT, dG, dC). Increased spectral intensity could also be observed near 1335 cm-1 (dA, dG) for CaDNA. Optical densitometry, employed to detect DNA aggregation, reveals increased turbidity during the melting transition for all divalent DNA-metal complexes, except SrDNA and BaDNA. Turbidity was not observed for DNA in the absence of metal. A correlation was made between DNA melting, aggregation, and the ratio of Raman intensities I1335/I1374. At room temperature, DNA-metal interactions result in a pH drop of 1.2-2.2 units for alkaline earths and more than 2.5 units for transition metals. Sr2+, Ba2+, and Mg2+ cause protonated sites on the DNA to become thermally labile. These results lead to a model that describes DNA aggregation and denaturation during heating in the presence of divalent metal cations; 1) The cations initially interact with the DNA at phosphate and/or base sites, resulting in proton displacement. 2) A combination of metal-base interactions and heating disrupts the base pairing within the DNA duplex. This allows divalent metals and protons to bind to additional sites on the DNA bases during the aggregation/melting process. 3) Strands whose bases have swung open upon disruption are linke...

Low specificity of metal ion binding in the metal ion core of a folded RNA

“…Data from Pearson (1988) and Feig and Uhlenbeck (1999 2+ . It may result from additional interactions with the P4-P6 RNA at sites other than the metal ion core; Mn 2+ has a higher affinity for the N7 of purines than do alkaline earth ions (Duguid et al 1995 , the two largest metal ions probed (Table 1). A possible model is as follows.…”

Condensation of nonstochiometric DNA/polycation complexes by divalent cations

“…In terms of the type of divalent cation, transition metals were somewhat more efficient than alkali earth metals probably because they bind DNA stronger as a result of additional coordination with bases. 25 Given that only 2-3 mM of the divalent cation was required for the effect, the concentrations are physiologically relevant. The extracellular concentration of Ca 2+ is 3 mM and the intracellular Mg 2+ total concentration is 10-15 mM.…”

Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes

“…The effects of divalent cations (Sr 2C , Ba 2C , Mg 2C , Mn 2C , Co 2C , Ni 2C and Cd 2C ) on the thermal denaturation of 160 bp DNA have also been documented. 127 All alkaline earth metals plus Mn 2C elevate the melting temperature (T m ) of DNA, whereas Co 2C , Ni 2C and Cd 2C lower T m . Additionally, Sr 2C , Ba 2C and Mg 2C cause protonated sites of DNA to become thermally labile.…”