Secondary structure effects on the interaction of different polynucleotides with Ca²⁺

Abstract

School for Advanced Studies, 1-341 27 Trieste, and 31nstitute of Biology, University of Udine, 1-331 00 Udine, Italy SYNOPSISThe interaction of Ca2+ ions in 10 m M NaCl at 17OC with polynucleotides of different primary and secondary structure has been investigated. The experimental results show the following:1. The affinity for calcium ion depends on the secondary structure of the polynucleotide and not, within the experimental error, on the base sequence.2. The following hierarchy in calcium ion binding can be established A-RNAs > BDNAs > single-stranded RNAs. The polyG binding curve is analogous to that of ARNAs; this strongly suggests that it does not adopt a single-stranded structure in our experimental conditions. 3. Apart from the case of single-stranded RNAs, where both Manning's and PoissonBoltzmann models seem to fit the data well, the Poisson-Boltzmann equation reproduces the experimental points better than the Manning's theory, which overestimates the affinity of the double-stranded nucleic acids for calcium ion.

A Gel Electrophoresis Study of the Competitive Effects of Monovalent Counterion on the Extent of Divalent Counterions Binding to DNA

“…In the former paper (Langlais et al, 1990), Raman spectroscopy shows that Mg 2ϩ and Ca 2ϩ interact dominantly with charged phosphates and very little with the bases. The other study shows that Ca 2ϩ binding to DNA is independent of base sequence and can be interpreted by polyelectrolyte theory (Manzini et al, 1990). Our data of Ca 2ϩ binding to the DNA fragments (Li et al, 1997) is well interpreted by Manning's CC theory, which includes only phosphate interactions, thus supporting the above obervation.…”

“…The result is not surprising, because quite a few studies (Eichhorn and Shin, 1968;Daune, 1974;Langlais et al, 1990;Manzini et al, 1990;Re, 1991;Duguid et al, 1993Duguid et al, , 1995 showed that alkaline earth metal cations and transition metal cations have different mechanisms of interacting with and binding to double-stranded DNA. From previous studies (Langlais et al, 1990;Manzini et al, 1990) it was concluded that alkaline earth cations interact primarily with DNA phosphates, resulting in stabilization of the double helix via reduction of electrostatic repulsion. In the former paper (Langlais et al, 1990), Raman spectroscopy shows that Mg 2ϩ and Ca 2ϩ interact dominantly with charged phosphates and very little with the bases.…”

“…Over the last two decades much attention has been paid (Eichhorn and Shin, 1968;Granot and Kearns, 1982;Rhee and Ware, 1983;Braunlin et al, 1989;Langlais et al, 1990;Duguid et al, 1995;Duguid and Bloomfield, 1996;Labarbe et al, 1996;Li et al, 1997) to the investigation of divalent metal cations binding to DNA, in the presence or absence of monovalent counterions, because of the importance of this problem from both a biological (Granot and Kearns, 1982;Manzini et al, 1990;Labarbe et al, 1996) and theoretical perspective (Manning, 1977(Manning, , 1978(Manning, , 1981. Our focus, in the general area of interaction of divalent metal cations with DNA in aqueous solution, is on understanding the nature of counterion binding to polyelectrolyte DNA.…”

“…The measured mobility reductions expressed as total fraction of charge neutralization were found to agree well with those calculated from Manning's CC theory. Previous papers have studied divalent and univalent counterion competition binding to DNA (Granot and Kearns, 1982;Rhee and Ware, 1983;Manzini et al, 1990;Ma and Bloomfield, 1995). Some of these studies compared experimental results with Manning's CC theory, but only qualitative agreement was reached (Rhee and Ware, 1983;Manzini et al, 1990).…”

“…Previous papers have studied divalent and univalent counterion competition binding to DNA (Granot and Kearns, 1982;Rhee and Ware, 1983;Manzini et al, 1990;Ma and Bloomfield, 1995). Some of these studies compared experimental results with Manning's CC theory, but only qualitative agreement was reached (Rhee and Ware, 1983;Manzini et al, 1990). One study (Granot and Kearns, 1982) reported data on the interaction of DNA with divalent Mn 2ϩ and compared their data with two theoretical approaches: Manning's CC theory and the Poisson-Boltzmann (PB) equation.…”