A Comparative Study of DNA Complexation with Mg(II) and Ca(II) in Aqueous Solution: Major and Minor Grooves Bindings

Abstract

Although structural differences for the Mg-DNA and Ca-DNA complexes are provided in the solid state, such comparative study in aqueous solution has been less investigated. The aim of this study was to examine the bindings of Mg and Ca cations with calf thymus DNA in aqueous solution at physiological pH, using constant concentration of DNA (1.25 or 12.5 mM) and various concentrations of metal ions (2 microM-650 microM). Capillary electrophoresis, UV-visible, and Fourier transform infrared spectroscopic methods were used to determine the cation-binding modes, the binding constants, and DNA structural variations in aqueous solution. Direct Ca-PO(2) binding was evident by major spectral changes (shifting and splitting) of the backbone PO(2) asymmetric stretching at 1222 cm(-1) with K = 4.80 x 10(5) M(-1), whereas an indirect Mg-phosphate interaction occurred (due to the lack of shifting and splitting of the phosphate band at 1222 cm(-1)) with K = 5.6 x 10(4) M(-1). The metal-base bindings were directly for the Mg with K = 3.20 x 10(5) M(-1) and indirectly for the Ca cation with K = 3.0 x 10(4) M(-1). Both major and minor groove bindings were observed with no alteration of the B-DNA conformation.

Extracting water and ion distributions from solution x-ray scattering experiments

“…(See the Appendix for the relationship between our analysis and the method from Meisburger et al) It is not clear how accurate this assumption is or whether the same assumption would be valid for highly charged ions (such as Mg 2+ and Sr 2+ ) since the interaction between those ions with nucleic acids is expected to be ion-dependent. [37][38][39][40][41][42] Here, we apply our analysis method to a 25 base-pair duplex DNA. Fig.…”

Thorium speciation in seawater

“…For example, Mg(II) and Ca (II) play a role in the complex formation of ATP and DNA, where they, as well as other metal ions, play a critical role in conformation stabilization (Ahmad et al, 2003;Deng et al, 2000). Given the similar ionic radii of Th(IV) and Ca(II) (i.e., 119 pm for Th(IV) and 126 pm for Ca(II) in 8-fold coordination, 108 pm for Th(IV) and 114 pm for Ca(II) in 6-fold coordination), it is possible that Th(IV) exchanges for Ca(II) in its coordination environments (e.g., the eggbox; Rees, 1972;Kohn, 1972;Moe et al, 1995), even though coulombic repulsion is about four times higher for Th(IV) (due to the higher charge/radius ratio).…”

Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I

“…We initially considered Tris as a buffer as it is commonly used as a medium for studies of metal ion-DNA interactions with DNA [11,12,21] and is particularly suitable for capillary electrophoresis experiments owing to its low conductivity [22]. However, transition metal ions form complexes of reasonable stability with Tris [20,[23][24][25][26][27][28][29] and ternary M(DNA)(Tris) complexes with oligonucleotides or DNA [16,20].…”

“…Although ACE investigations of metal ion-DNA interactions have been reported, only a few studies describe the quantification of complex equilibria. Apparent equilibrium constants have been determined for the interactions of Ag + [11], Mg 2+ [12], Ca 2+ [12] and Fe 2+ [13] salts with double-stranded DNA. Two different modes of capillary electrophoresis, electrophoretic mobility shift assay (EMSA) and peak area evaluation, are commonly used.…”